Starting phenix.real_space_refine on Sat Jan 18 01:11:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w0i_43710/01_2025/8w0i_43710_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w0i_43710/01_2025/8w0i_43710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w0i_43710/01_2025/8w0i_43710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w0i_43710/01_2025/8w0i_43710.map" model { file = "/net/cci-nas-00/data/ceres_data/8w0i_43710/01_2025/8w0i_43710_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w0i_43710/01_2025/8w0i_43710_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 5 6.06 5 P 14 5.49 5 Mg 5 5.21 5 S 173 5.16 5 C 17800 2.51 5 N 5023 2.21 5 O 5361 1.98 5 H 28489 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 56870 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 9471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 9471 Classifications: {'peptide': 598} Link IDs: {'PTRANS': 26, 'TRANS': 571} Chain breaks: 6 Chain: "3" Number of atoms: 9354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 9354 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain breaks: 4 Chain: "4" Number of atoms: 9311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9311 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 25, 'TRANS': 554} Chain breaks: 5 Chain: "5" Number of atoms: 9327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 9327 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 26, 'TRANS': 560} Chain breaks: 8 Chain: "6" Number of atoms: 9497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 9497 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 20, 'TRANS': 570} Chain breaks: 3 Chain: "7" Number of atoms: 9749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 9749 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 27, 'TRANS': 579} Chain breaks: 6 Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2379 SG CYS 2 329 79.418 89.440 67.017 1.00211.95 S ATOM 2425 SG CYS 2 332 83.415 88.638 66.300 1.00190.21 S ATOM 2594 SG CYS 2 352 80.611 85.983 66.542 1.00192.53 S ATOM 2633 SG CYS 2 355 81.752 87.813 69.519 1.00214.79 S ATOM 21141 SG CYS 4 306 97.248 86.143 49.085 1.00201.73 S ATOM 21184 SG CYS 4 309 100.144 85.564 46.705 1.00192.70 S ATOM 21473 SG CYS 4 328 100.814 86.496 50.225 1.00193.40 S ATOM 21514 SG CYS 4 331 99.596 89.159 47.878 1.00216.43 S ATOM 30525 SG CYS 5 172 94.725 125.308 84.002 1.00265.25 S ATOM 30570 SG CYS 5 175 97.816 126.728 84.377 1.00251.17 S ATOM 30921 SG CYS 5 197 96.352 129.519 83.264 1.00199.35 S ATOM 39820 SG CYS 6 158 82.441 95.214 49.126 1.00280.08 S ATOM 39861 SG CYS 6 161 84.325 96.571 46.684 1.00273.59 S ATOM 40179 SG CYS 6 180 85.540 95.447 50.787 1.00271.41 S ATOM 40257 SG CYS 6 185 84.492 98.722 49.657 1.00270.60 S ATOM 49909 SG CYS 7 184 113.177 85.522 77.709 1.00184.37 S ATOM 49948 SG CYS 7 187 115.847 86.007 80.225 1.00186.36 S ATOM 50237 SG CYS 7 206 113.034 88.700 79.556 1.00192.18 S ATOM 50304 SG CYS 7 211 115.804 88.159 77.047 1.00220.79 S Time building chain proxies: 25.28, per 1000 atoms: 0.44 Number of scatterers: 56870 At special positions: 0 Unit cell: (133.952, 163.072, 154.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 S 173 16.00 P 14 15.00 Mg 5 11.99 O 5361 8.00 N 5023 7.00 C 17800 6.00 H 28489 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.43 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21000 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 355 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 352 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 329 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 332 " pdb=" ZN 41000 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 309 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 328 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 331 " pdb=" ZN 51000 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 175 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 172 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 197 " pdb=" ZN 61000 " pdb="ZN ZN 61000 " - pdb=" SG CYS 6 158 " pdb="ZN ZN 61000 " - pdb=" SG CYS 6 180 " pdb="ZN ZN 61000 " - pdb=" SG CYS 6 185 " pdb="ZN ZN 61000 " - pdb=" SG CYS 6 161 " pdb=" ZN 71000 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 184 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 211 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 206 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 187 " Number of angles added : 24 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6778 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 34 sheets defined 46.2% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain '2' and resid 181 through 188 Processing helix chain '2' and resid 188 through 206 removed outlier: 3.632A pdb=" N ARG 2 204 " --> pdb=" O LYS 2 200 " (cutoff:3.500A) Processing helix chain '2' and resid 213 through 226 removed outlier: 3.694A pdb=" N GLU 2 225 " --> pdb=" O ASP 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 234 through 241 Processing helix chain '2' and resid 242 through 251 Proline residue: 2 249 - end of helix Processing helix chain '2' and resid 251 through 271 Processing helix chain '2' and resid 293 through 297 removed outlier: 3.530A pdb=" N LEU 2 297 " --> pdb=" O LEU 2 294 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 302 Processing helix chain '2' and resid 447 through 451 removed outlier: 3.875A pdb=" N VAL 2 451 " --> pdb=" O ASP 2 448 " (cutoff:3.500A) Processing helix chain '2' and resid 457 through 470 Processing helix chain '2' and resid 472 through 481 Processing helix chain '2' and resid 488 through 501 Processing helix chain '2' and resid 528 through 540 Processing helix chain '2' and resid 574 through 580 Processing helix chain '2' and resid 593 through 607 Processing helix chain '2' and resid 650 through 656 removed outlier: 3.623A pdb=" N ARG 2 656 " --> pdb=" O PRO 2 652 " (cutoff:3.500A) Processing helix chain '2' and resid 668 through 686 Processing helix chain '2' and resid 687 through 691 removed outlier: 3.796A pdb=" N LYS 2 691 " --> pdb=" O PRO 2 688 " (cutoff:3.500A) Processing helix chain '2' and resid 716 through 731 Processing helix chain '2' and resid 739 through 754 Processing helix chain '2' and resid 763 through 781 removed outlier: 3.718A pdb=" N ILE 2 767 " --> pdb=" O THR 2 763 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 805 removed outlier: 4.121A pdb=" N VAL 2 791 " --> pdb=" O ILE 2 787 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN 2 792 " --> pdb=" O GLU 2 788 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 818 Processing helix chain '2' and resid 818 through 825 removed outlier: 4.134A pdb=" N ARG 2 825 " --> pdb=" O TYR 2 821 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 24 Processing helix chain '3' and resid 30 through 43 Processing helix chain '3' and resid 51 through 58 Processing helix chain '3' and resid 58 through 68 Processing helix chain '3' and resid 69 through 88 Processing helix chain '3' and resid 88 through 95 removed outlier: 3.592A pdb=" N TYR 3 95 " --> pdb=" O TYR 3 91 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 121 Processing helix chain '3' and resid 224 through 226 No H-bonds generated for 'chain '3' and resid 224 through 226' Processing helix chain '3' and resid 277 through 291 removed outlier: 3.946A pdb=" N ARG 3 291 " --> pdb=" O PHE 3 287 " (cutoff:3.500A) Processing helix chain '3' and resid 291 through 302 removed outlier: 4.680A pdb=" N PHE 3 296 " --> pdb=" O SER 3 292 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP 3 297 " --> pdb=" O LYS 3 293 " (cutoff:3.500A) Processing helix chain '3' and resid 310 through 323 Processing helix chain '3' and resid 350 through 362 Processing helix chain '3' and resid 396 through 401 Processing helix chain '3' and resid 411 through 414 Processing helix chain '3' and resid 415 through 429 removed outlier: 3.942A pdb=" N HIS 3 423 " --> pdb=" O ARG 3 419 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL 3 425 " --> pdb=" O ALA 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 434 through 438 removed outlier: 3.550A pdb=" N GLY 3 437 " --> pdb=" O ALA 3 434 " (cutoff:3.500A) Processing helix chain '3' and resid 464 through 470 Processing helix chain '3' and resid 473 through 479 Processing helix chain '3' and resid 490 through 507 Processing helix chain '3' and resid 564 through 578 removed outlier: 3.898A pdb=" N ILE 3 577 " --> pdb=" O HIS 3 573 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE 3 578 " --> pdb=" O VAL 3 574 " (cutoff:3.500A) Processing helix chain '3' and resid 583 through 601 Processing helix chain '3' and resid 614 through 632 Processing helix chain '3' and resid 638 through 654 Processing helix chain '4' and resid 158 through 172 Processing helix chain '4' and resid 192 through 204 removed outlier: 3.550A pdb=" N VAL 4 202 " --> pdb=" O GLY 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 219 Processing helix chain '4' and resid 219 through 229 Processing helix chain '4' and resid 229 through 248 Proline residue: 4 235 - end of helix Processing helix chain '4' and resid 275 through 279 Processing helix chain '4' and resid 442 through 455 removed outlier: 3.702A pdb=" N LYS 4 455 " --> pdb=" O GLU 4 451 " (cutoff:3.500A) Processing helix chain '4' and resid 457 through 466 Processing helix chain '4' and resid 474 through 486 Processing helix chain '4' and resid 515 through 525 Processing helix chain '4' and resid 561 through 566 Processing helix chain '4' and resid 580 through 594 Processing helix chain '4' and resid 629 through 635 Processing helix chain '4' and resid 637 through 644 removed outlier: 3.705A pdb=" N PHE 4 644 " --> pdb=" O LEU 4 640 " (cutoff:3.500A) Processing helix chain '4' and resid 655 through 671 Processing helix chain '4' and resid 683 through 698 removed outlier: 3.594A pdb=" N LEU 4 687 " --> pdb=" O ASP 4 683 " (cutoff:3.500A) Processing helix chain '4' and resid 703 through 723 removed outlier: 4.130A pdb=" N SER 4 723 " --> pdb=" O LYS 4 719 " (cutoff:3.500A) Processing helix chain '4' and resid 730 through 749 removed outlier: 3.540A pdb=" N LEU 4 734 " --> pdb=" O TYR 4 730 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 773 Processing helix chain '5' and resid 27 through 42 Processing helix chain '5' and resid 53 through 65 Processing helix chain '5' and resid 74 through 81 Processing helix chain '5' and resid 81 through 91 removed outlier: 3.547A pdb=" N ALA 5 85 " --> pdb=" O ASP 5 81 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 111 removed outlier: 3.668A pdb=" N HIS 5 95 " --> pdb=" O GLN 5 91 " (cutoff:3.500A) Processing helix chain '5' and resid 141 through 145 Processing helix chain '5' and resid 315 through 328 Processing helix chain '5' and resid 330 through 339 Processing helix chain '5' and resid 348 through 359 Processing helix chain '5' and resid 386 through 398 removed outlier: 3.595A pdb=" N LEU 5 390 " --> pdb=" O ALA 5 386 " (cutoff:3.500A) Processing helix chain '5' and resid 432 through 437 Processing helix chain '5' and resid 446 through 450 removed outlier: 3.704A pdb=" N MET 5 450 " --> pdb=" O PHE 5 447 " (cutoff:3.500A) Processing helix chain '5' and resid 451 through 464 removed outlier: 4.000A pdb=" N HIS 5 459 " --> pdb=" O ARG 5 455 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU 5 460 " --> pdb=" O VAL 5 456 " (cutoff:3.500A) Processing helix chain '5' and resid 508 through 512 removed outlier: 3.917A pdb=" N SER 5 512 " --> pdb=" O PRO 5 508 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 508 through 512' Processing helix chain '5' and resid 555 through 570 Processing helix chain '5' and resid 575 through 593 Processing helix chain '5' and resid 609 through 627 removed outlier: 3.683A pdb=" N LYS 5 627 " --> pdb=" O LEU 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 658 Processing helix chain '5' and resid 666 through 683 Processing helix chain '5' and resid 691 through 701 Processing helix chain '5' and resid 704 through 718 Processing helix chain '6' and resid 20 through 37 Processing helix chain '6' and resid 44 through 54 removed outlier: 3.675A pdb=" N GLN 6 48 " --> pdb=" O ILE 6 44 " (cutoff:3.500A) Processing helix chain '6' and resid 65 through 72 Processing helix chain '6' and resid 72 through 82 Processing helix chain '6' and resid 82 through 100 Proline residue: 6 88 - end of helix removed outlier: 3.516A pdb=" N ASP 6 100 " --> pdb=" O THR 6 96 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 126 Processing helix chain '6' and resid 127 through 131 Processing helix chain '6' and resid 231 through 233 No H-bonds generated for 'chain '6' and resid 231 through 233' Processing helix chain '6' and resid 322 through 329 Processing helix chain '6' and resid 330 through 343 Processing helix chain '6' and resid 345 through 355 Processing helix chain '6' and resid 361 through 374 Processing helix chain '6' and resid 401 through 413 Processing helix chain '6' and resid 447 through 452 Processing helix chain '6' and resid 461 through 465 removed outlier: 3.517A pdb=" N MET 6 465 " --> pdb=" O PHE 6 462 " (cutoff:3.500A) Processing helix chain '6' and resid 466 through 480 Processing helix chain '6' and resid 515 through 520 Processing helix chain '6' and resid 523 through 529 Processing helix chain '6' and resid 541 through 558 Processing helix chain '6' and resid 568 through 581 removed outlier: 3.728A pdb=" N GLN 6 581 " --> pdb=" O LEU 6 577 " (cutoff:3.500A) Processing helix chain '6' and resid 587 through 605 removed outlier: 3.661A pdb=" N ASP 6 605 " --> pdb=" O LEU 6 601 " (cutoff:3.500A) Processing helix chain '6' and resid 617 through 636 removed outlier: 3.788A pdb=" N HIS 6 635 " --> pdb=" O MET 6 631 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 656 Processing helix chain '7' and resid 5 through 19 Processing helix chain '7' and resid 25 through 27 No H-bonds generated for 'chain '7' and resid 25 through 27' Processing helix chain '7' and resid 31 through 42 removed outlier: 3.894A pdb=" N GLN 7 36 " --> pdb=" O LYS 7 32 " (cutoff:3.500A) Processing helix chain '7' and resid 52 through 57 Processing helix chain '7' and resid 59 through 69 Processing helix chain '7' and resid 69 through 89 removed outlier: 4.026A pdb=" N TYR 7 73 " --> pdb=" O ASN 7 69 " (cutoff:3.500A) Proline residue: 7 86 - end of helix Processing helix chain '7' and resid 96 through 112 removed outlier: 3.801A pdb=" N ASP 7 100 " --> pdb=" O LYS 7 96 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL 7 101 " --> pdb=" O ASP 7 97 " (cutoff:3.500A) Processing helix chain '7' and resid 127 through 131 Processing helix chain '7' and resid 148 through 152 Processing helix chain '7' and resid 153 through 157 Processing helix chain '7' and resid 208 through 215 Processing helix chain '7' and resid 260 through 262 No H-bonds generated for 'chain '7' and resid 260 through 262' Processing helix chain '7' and resid 320 through 329 Processing helix chain '7' and resid 330 through 340 removed outlier: 4.710A pdb=" N GLU 7 334 " --> pdb=" O GLU 7 330 " (cutoff:3.500A) Processing helix chain '7' and resid 347 through 360 Processing helix chain '7' and resid 386 through 398 Processing helix chain '7' and resid 432 through 438 removed outlier: 3.631A pdb=" N ASP 7 438 " --> pdb=" O LEU 7 434 " (cutoff:3.500A) Processing helix chain '7' and resid 446 through 450 Processing helix chain '7' and resid 451 through 465 Processing helix chain '7' and resid 508 through 515 removed outlier: 3.710A pdb=" N PHE 7 515 " --> pdb=" O LEU 7 511 " (cutoff:3.500A) Processing helix chain '7' and resid 526 through 544 Processing helix chain '7' and resid 555 through 569 removed outlier: 3.919A pdb=" N LYS 7 569 " --> pdb=" O MET 7 565 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 595 removed outlier: 3.639A pdb=" N ALA 7 578 " --> pdb=" O PRO 7 574 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP 7 579 " --> pdb=" O GLU 7 575 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR 7 580 " --> pdb=" O SER 7 576 " (cutoff:3.500A) Processing helix chain '7' and resid 602 through 621 removed outlier: 3.555A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 644 Processing sheet with id=AA1, first strand: chain '2' and resid 229 through 233 removed outlier: 5.852A pdb=" N LEU 2 230 " --> pdb=" O ARG 2 284 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N SER 2 286 " --> pdb=" O LEU 2 230 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL 2 232 " --> pdb=" O SER 2 286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 558 through 562 removed outlier: 6.461A pdb=" N THR 2 313 " --> pdb=" O ALA 2 573 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN 2 304 " --> pdb=" O TYR 2 418 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR 2 415 " --> pdb=" O ASN 2 442 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN 2 421 " --> pdb=" O ALA 2 436 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N THR 2 437 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP 2 395 " --> pdb=" O THR 2 437 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU 2 399 " --> pdb=" O ALA 2 441 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N HIS 2 443 " --> pdb=" O LEU 2 399 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG 2 375 " --> pdb=" O CYS 2 315 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS 2 315 " --> pdb=" O ARG 2 375 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG 2 377 " --> pdb=" O THR 2 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 339 through 341 removed outlier: 6.925A pdb=" N LEU 2 322 " --> pdb=" O THR 2 368 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR 2 368 " --> pdb=" O LEU 2 322 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N MET 2 324 " --> pdb=" O GLU 2 366 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU 2 366 " --> pdb=" O MET 2 324 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS 2 326 " --> pdb=" O ASN 2 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 629 through 630 removed outlier: 7.755A pdb=" N ALA 2 630 " --> pdb=" O VAL 2 519 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU 2 521 " --> pdb=" O ALA 2 630 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU 2 520 " --> pdb=" O CYS 2 661 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL 2 663 " --> pdb=" O LEU 2 520 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS 2 522 " --> pdb=" O VAL 2 663 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain '2' and resid 543 through 547 Processing sheet with id=AA6, first strand: chain '2' and resid 608 through 613 Processing sheet with id=AA7, first strand: chain '3' and resid 46 through 50 removed outlier: 6.072A pdb=" N LEU 3 47 " --> pdb=" O GLY 3 101 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLU 3 103 " --> pdb=" O LEU 3 47 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL 3 49 " --> pdb=" O GLU 3 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain '3' and resid 110 through 111 removed outlier: 7.332A pdb=" N VAL 3 111 " --> pdb=" O GLU 3 128 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N ILE 3 130 " --> pdb=" O VAL 3 111 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 124 through 135 current: chain '3' and resid 153 through 158 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 153 through 158 current: chain '3' and resid 216 through 222 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 216 through 222 current: chain '3' and resid 258 through 267 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 258 through 267 current: chain '3' and resid 391 through 394 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '3' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain '3' and resid 365 through 369 removed outlier: 6.611A pdb=" N ILE 3 366 " --> pdb=" O CYS 3 407 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ASP 3 409 " --> pdb=" O ILE 3 366 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR 3 368 " --> pdb=" O ASP 3 409 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL 3 406 " --> pdb=" O LEU 3 449 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ALA 3 451 " --> pdb=" O VAL 3 406 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE 3 408 " --> pdb=" O ALA 3 451 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE 3 341 " --> pdb=" O ALA 3 450 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA 3 452 " --> pdb=" O ILE 3 341 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU 3 343 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 3 342 " --> pdb=" O PHE 3 483 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N MET 3 485 " --> pdb=" O LEU 3 342 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE 3 344 " --> pdb=" O MET 3 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain '3' and resid 430 through 433 Processing sheet with id=AB3, first strand: chain '4' and resid 208 through 211 removed outlier: 6.668A pdb=" N LEU 4 208 " --> pdb=" O ARG 4 261 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE 4 263 " --> pdb=" O LEU 4 208 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL 4 210 " --> pdb=" O PHE 4 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain '4' and resid 282 through 291 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 282 through 291 current: chain '4' and resid 313 through 316 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 313 through 316 current: chain '4' and resid 369 through 375 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 369 through 375 current: chain '4' and resid 413 through 423 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain '4' and resid 408 through 409 Processing sheet with id=AB6, first strand: chain '4' and resid 531 through 534 removed outlier: 6.592A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ASP 4 574 " --> pdb=" O GLN 4 531 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR 4 533 " --> pdb=" O ASP 4 574 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N CYS 4 571 " --> pdb=" O LEU 4 614 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA 4 616 " --> pdb=" O CYS 4 571 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE 4 573 " --> pdb=" O ALA 4 616 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 546 through 549 Processing sheet with id=AB8, first strand: chain '4' and resid 595 through 600 Processing sheet with id=AB9, first strand: chain '5' and resid 44 through 46 Processing sheet with id=AC1, first strand: chain '5' and resid 69 through 73 removed outlier: 5.570A pdb=" N ILE 5 70 " --> pdb=" O MET 5 127 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS 5 129 " --> pdb=" O ILE 5 70 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL 5 72 " --> pdb=" O LYS 5 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain '5' and resid 148 through 159 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 148 through 159 current: chain '5' and resid 178 through 183 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 178 through 183 current: chain '5' and resid 244 through 249 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 244 through 249 current: chain '5' and resid 293 through 301 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 293 through 301 current: chain '5' and resid 426 through 430 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain '5' and resid 363 through 364 removed outlier: 3.503A pdb=" N LYS 5 363 " --> pdb=" O ARG 5 371 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '5' and resid 401 through 405 removed outlier: 6.330A pdb=" N VAL 5 442 " --> pdb=" O LEU 5 485 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA 5 487 " --> pdb=" O VAL 5 442 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE 5 444 " --> pdb=" O ALA 5 487 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU 5 377 " --> pdb=" O ALA 5 486 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA 5 488 " --> pdb=" O LEU 5 377 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N MET 5 379 " --> pdb=" O ALA 5 488 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU 5 378 " --> pdb=" O PHE 5 518 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '5' and resid 466 through 471 Processing sheet with id=AC6, first strand: chain '5' and resid 573 through 574 removed outlier: 7.021A pdb=" N ARG 5 573 " --> pdb=" O ALA 5 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain '6' and resid 60 through 64 removed outlier: 6.211A pdb=" N LEU 6 61 " --> pdb=" O ALA 6 113 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN 6 115 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL 6 63 " --> pdb=" O GLN 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '6' and resid 120 through 121 removed outlier: 4.359A pdb=" N SER 6 138 " --> pdb=" O HIS 6 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '6' and resid 134 through 144 current: chain '6' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 164 through 169 current: chain '6' and resid 223 through 229 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 223 through 229 current: chain '6' and resid 294 through 305 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 294 through 305 current: chain '6' and resid 442 through 445 Processing sheet with id=AC9, first strand: chain '6' and resid 378 through 379 Processing sheet with id=AD1, first strand: chain '6' and resid 416 through 420 removed outlier: 6.285A pdb=" N CYS 6 457 " --> pdb=" O LEU 6 500 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALA 6 502 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE 6 459 " --> pdb=" O ALA 6 502 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL 6 392 " --> pdb=" O ALA 6 501 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ALA 6 503 " --> pdb=" O VAL 6 392 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE 6 394 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS 6 393 " --> pdb=" O PHE 6 534 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU 6 536 " --> pdb=" O CYS 6 393 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL 6 395 " --> pdb=" O LEU 6 536 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 481 through 486 Processing sheet with id=AD3, first strand: chain '7' and resid 22 through 24 removed outlier: 3.723A pdb=" N GLN 7 30 " --> pdb=" O GLN 7 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '7' and resid 47 through 51 Processing sheet with id=AD5, first strand: chain '7' and resid 160 through 171 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 160 through 171 current: chain '7' and resid 190 through 194 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 190 through 194 current: chain '7' and resid 252 through 258 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 252 through 258 current: chain '7' and resid 295 through 305 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 295 through 305 current: chain '7' and resid 428 through 430 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '7' and resid 401 through 404 removed outlier: 6.453A pdb=" N GLN 7 402 " --> pdb=" O CYS 7 443 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE 7 377 " --> pdb=" O ALA 7 486 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ALA 7 488 " --> pdb=" O ILE 7 377 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU 7 379 " --> pdb=" O ALA 7 488 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYS 7 378 " --> pdb=" O TRP 7 519 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE 7 521 " --> pdb=" O CYS 7 378 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET 7 380 " --> pdb=" O ILE 7 521 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '7' and resid 466 through 469 1179 hydrogen bonds defined for protein. 3402 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: 21.32 Time building geometry restraints manager: 15.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 28436 1.03 - 1.23: 653 1.23 - 1.43: 11110 1.43 - 1.63: 16847 1.63 - 1.82: 274 Bond restraints: 57320 Sorted by residual: bond pdb=" CB CYS 6 180 " pdb=" SG CYS 6 180 " ideal model delta sigma weight residual 1.808 1.740 0.068 3.30e-02 9.18e+02 4.28e+00 bond pdb=" CA SER 6 399 " pdb=" CB SER 6 399 " ideal model delta sigma weight residual 1.530 1.505 0.025 1.69e-02 3.50e+03 2.22e+00 bond pdb=" CA TYR 2 785 " pdb=" C TYR 2 785 " ideal model delta sigma weight residual 1.525 1.511 0.014 1.02e-02 9.61e+03 1.90e+00 bond pdb=" C4 ADP 31002 " pdb=" C5 ADP 31002 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C1' ATP 61002 " pdb=" O4' ATP 61002 " ideal model delta sigma weight residual 1.416 1.400 0.016 1.30e-02 5.92e+03 1.57e+00 ... (remaining 57315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 103420 2.19 - 4.38: 270 4.38 - 6.57: 33 6.57 - 8.76: 1 8.76 - 10.95: 1 Bond angle restraints: 103725 Sorted by residual: angle pdb=" N GLY 5 655 " pdb=" CA GLY 5 655 " pdb=" C GLY 5 655 " ideal model delta sigma weight residual 112.77 106.37 6.40 1.28e+00 6.10e-01 2.50e+01 angle pdb=" N VAL 3 142 " pdb=" CA VAL 3 142 " pdb=" C VAL 3 142 " ideal model delta sigma weight residual 112.96 109.38 3.58 1.00e+00 1.00e+00 1.28e+01 angle pdb=" C1' ATP 71002 " pdb=" O4' ATP 71002 " pdb=" C4' ATP 71002 " ideal model delta sigma weight residual 109.40 103.93 5.47 1.61e+00 3.87e-01 1.16e+01 angle pdb=" C1' ATP 21002 " pdb=" O4' ATP 21002 " pdb=" C4' ATP 21002 " ideal model delta sigma weight residual 109.40 104.09 5.31 1.61e+00 3.87e-01 1.09e+01 angle pdb=" N GLU 7 502 " pdb=" CA GLU 7 502 " pdb=" CB GLU 7 502 " ideal model delta sigma weight residual 114.17 111.04 3.13 1.14e+00 7.69e-01 7.55e+00 ... (remaining 103720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 25453 17.51 - 35.03: 966 35.03 - 52.54: 316 52.54 - 70.06: 67 70.06 - 87.57: 12 Dihedral angle restraints: 26814 sinusoidal: 15015 harmonic: 11799 Sorted by residual: dihedral pdb=" O1B ADP 31002 " pdb=" O3A ADP 31002 " pdb=" PB ADP 31002 " pdb=" PA ADP 31002 " ideal model delta sinusoidal sigma weight residual -60.00 -142.25 82.24 1 2.00e+01 2.50e-03 2.08e+01 dihedral pdb=" CA GLY 5 381 " pdb=" C GLY 5 381 " pdb=" N ASP 5 382 " pdb=" CA ASP 5 382 " ideal model delta harmonic sigma weight residual 180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ARG 7 133 " pdb=" C ARG 7 133 " pdb=" N PHE 7 134 " pdb=" CA PHE 7 134 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 26811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3841 0.058 - 0.117: 509 0.117 - 0.175: 60 0.175 - 0.233: 3 0.233 - 0.292: 9 Chirality restraints: 4422 Sorted by residual: chirality pdb=" C3' ATP 21002 " pdb=" C2' ATP 21002 " pdb=" C4' ATP 21002 " pdb=" O3' ATP 21002 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP 21002 " pdb=" C1' ATP 21002 " pdb=" C3' ATP 21002 " pdb=" O2' ATP 21002 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C3' ATP 41002 " pdb=" C2' ATP 41002 " pdb=" C4' ATP 41002 " pdb=" O3' ATP 41002 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 4419 not shown) Planarity restraints: 8383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN 2 506 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO 2 507 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO 2 507 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO 2 507 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY 5 571 " 0.032 5.00e-02 4.00e+02 4.75e-02 3.60e+00 pdb=" N PRO 5 572 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO 5 572 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO 5 572 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 5 382 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO 5 383 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO 5 383 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO 5 383 " 0.026 5.00e-02 4.00e+02 ... (remaining 8380 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 2635 2.18 - 2.78: 118506 2.78 - 3.39: 159290 3.39 - 3.99: 203124 3.99 - 4.60: 319798 Nonbonded interactions: 803353 Sorted by model distance: nonbonded pdb=" O PHE 6 156 " pdb=" H ILE 6 165 " model vdw 1.571 2.450 nonbonded pdb=" HZ1 LYS 7 387 " pdb=" OD1 ASN 7 489 " model vdw 1.573 2.450 nonbonded pdb=" HH TYR 6 575 " pdb=" O MET 6 634 " model vdw 1.583 2.450 nonbonded pdb=" OE2 GLU 7 632 " pdb="HH21 ARG 7 635 " model vdw 1.591 2.450 nonbonded pdb=" HH TYR 4 690 " pdb=" O VAL 4 747 " model vdw 1.592 2.450 ... (remaining 803348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.540 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: 0.750 Extract box with map and model: 1.880 Check model and map are aligned: 0.330 Set scattering table: 0.420 Process input model: 119.290 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28831 Z= 0.196 Angle : 0.491 6.587 38910 Z= 0.262 Chirality : 0.042 0.292 4422 Planarity : 0.003 0.051 5007 Dihedral : 9.616 87.571 11123 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 3481 helix: 2.13 (0.14), residues: 1457 sheet: -0.27 (0.19), residues: 748 loop : -0.39 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 5 69 HIS 0.004 0.001 HIS 4 256 PHE 0.014 0.001 PHE 2 247 TYR 0.016 0.001 TYR 7 102 ARG 0.009 0.000 ARG 7 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 352 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue SER 403 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 600 ILE cc_start: 0.9413 (pp) cc_final: 0.9206 (tp) REVERT: 2 674 MET cc_start: 0.9400 (mmm) cc_final: 0.9014 (mmp) REVERT: 4 684 MET cc_start: 0.9057 (ptm) cc_final: 0.8842 (ppp) REVERT: 5 434 MET cc_start: 0.9111 (mmm) cc_final: 0.8606 (mmm) REVERT: 6 445 GLU cc_start: 0.8358 (tt0) cc_final: 0.7945 (tm-30) REVERT: 7 109 MET cc_start: 0.9407 (mmm) cc_final: 0.9107 (ttt) REVERT: 7 430 GLU cc_start: 0.8977 (tt0) cc_final: 0.8449 (pp20) REVERT: 7 438 ASP cc_start: 0.8648 (t0) cc_final: 0.8047 (t0) REVERT: 7 556 MET cc_start: 0.9359 (mtm) cc_final: 0.8934 (mtt) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.8865 time to fit residues: 305.4474 Evaluate side-chains 165 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 320 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 692 HIS 6 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.056731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.045134 restraints weight = 693586.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.047599 restraints weight = 303927.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.048314 restraints weight = 155339.104| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28831 Z= 0.203 Angle : 0.498 6.681 38910 Z= 0.260 Chirality : 0.039 0.143 4422 Planarity : 0.003 0.045 5007 Dihedral : 6.408 89.162 4039 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.48 % Allowed : 6.48 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3481 helix: 2.18 (0.14), residues: 1473 sheet: -0.58 (0.19), residues: 744 loop : -0.44 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 6 334 HIS 0.009 0.001 HIS 5 692 PHE 0.016 0.001 PHE 2 589 TYR 0.011 0.001 TYR 2 535 ARG 0.003 0.000 ARG 5 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 352 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue SER 403 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 674 MET cc_start: 0.9545 (mmm) cc_final: 0.9148 (mmp) REVERT: 2 793 MET cc_start: 0.8429 (mmp) cc_final: 0.8109 (mmp) REVERT: 3 423 HIS cc_start: 0.9113 (OUTLIER) cc_final: 0.8907 (t-90) REVERT: 4 271 MET cc_start: 0.7707 (mtp) cc_final: 0.7445 (mtp) REVERT: 4 288 MET cc_start: 0.8352 (ttp) cc_final: 0.8073 (ttt) REVERT: 4 684 MET cc_start: 0.9235 (ptm) cc_final: 0.8819 (ppp) REVERT: 5 434 MET cc_start: 0.9400 (mmm) cc_final: 0.8776 (mmm) REVERT: 5 445 ASP cc_start: 0.9244 (OUTLIER) cc_final: 0.8945 (m-30) REVERT: 6 445 GLU cc_start: 0.8456 (tt0) cc_final: 0.7827 (tm-30) REVERT: 7 109 MET cc_start: 0.9271 (mmm) cc_final: 0.9012 (ttt) REVERT: 7 205 MET cc_start: 0.8152 (mmm) cc_final: 0.7933 (mmm) REVERT: 7 430 GLU cc_start: 0.8816 (tt0) cc_final: 0.8327 (pp20) REVERT: 7 438 ASP cc_start: 0.8381 (t0) cc_final: 0.7691 (t0) REVERT: 7 450 MET cc_start: 0.8378 (mtp) cc_final: 0.8166 (mtp) outliers start: 15 outliers final: 9 residues processed: 176 average time/residue: 0.9236 time to fit residues: 252.3043 Evaluate side-chains 167 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 332 CYS Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 502 LEU Chi-restraints excluded: chain 4 residue 361 MET Chi-restraints excluded: chain 4 residue 368 HIS Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 6 residue 202 ASP Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 7 residue 118 MET Chi-restraints excluded: chain 7 residue 559 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 81 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 242 optimal weight: 0.0470 chunk 68 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 279 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 593 ASN ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.055956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.044243 restraints weight = 700514.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.046150 restraints weight = 296440.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.047332 restraints weight = 179668.664| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28831 Z= 0.287 Angle : 0.514 8.553 38910 Z= 0.272 Chirality : 0.039 0.149 4422 Planarity : 0.003 0.043 5007 Dihedral : 6.291 79.657 4039 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.74 % Allowed : 7.48 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3481 helix: 2.03 (0.14), residues: 1474 sheet: -0.84 (0.19), residues: 751 loop : -0.63 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 6 334 HIS 0.004 0.001 HIS 2 686 PHE 0.011 0.001 PHE 6 412 TYR 0.015 0.001 TYR 5 42 ARG 0.003 0.000 ARG 7 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 352 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue SER 403 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 674 MET cc_start: 0.9550 (mmm) cc_final: 0.9164 (mmp) REVERT: 2 793 MET cc_start: 0.8488 (mmp) cc_final: 0.8128 (mmp) REVERT: 3 423 HIS cc_start: 0.9114 (OUTLIER) cc_final: 0.8905 (t-90) REVERT: 4 271 MET cc_start: 0.7956 (mtp) cc_final: 0.7739 (mtp) REVERT: 4 684 MET cc_start: 0.9210 (ptm) cc_final: 0.8810 (ppp) REVERT: 5 445 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8903 (m-30) REVERT: 6 445 GLU cc_start: 0.8421 (tt0) cc_final: 0.7782 (tm-30) REVERT: 7 109 MET cc_start: 0.9278 (mmm) cc_final: 0.9018 (ttt) REVERT: 7 430 GLU cc_start: 0.8815 (tt0) cc_final: 0.8330 (pp20) REVERT: 7 438 ASP cc_start: 0.8565 (t0) cc_final: 0.7938 (t0) REVERT: 7 621 MET cc_start: 0.9154 (mmt) cc_final: 0.8768 (mmm) outliers start: 23 outliers final: 12 residues processed: 173 average time/residue: 0.8447 time to fit residues: 225.1371 Evaluate side-chains 161 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 332 CYS Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 795 ILE Chi-restraints excluded: chain 3 residue 13 ARG Chi-restraints excluded: chain 3 residue 111 VAL Chi-restraints excluded: chain 3 residue 423 HIS Chi-restraints excluded: chain 3 residue 502 LEU Chi-restraints excluded: chain 4 residue 361 MET Chi-restraints excluded: chain 4 residue 368 HIS Chi-restraints excluded: chain 4 residue 757 ASP Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 6 residue 202 ASP Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 7 residue 102 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 259 optimal weight: 0.9990 chunk 302 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 352 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.056125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.044425 restraints weight = 697892.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.046330 restraints weight = 294857.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.047524 restraints weight = 179191.171| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28831 Z= 0.219 Angle : 0.485 6.466 38910 Z= 0.253 Chirality : 0.039 0.141 4422 Planarity : 0.003 0.045 5007 Dihedral : 6.179 81.940 4039 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.51 % Allowed : 7.96 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3481 helix: 2.12 (0.14), residues: 1473 sheet: -0.98 (0.19), residues: 753 loop : -0.68 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 6 334 HIS 0.005 0.001 HIS 2 686 PHE 0.016 0.001 PHE 5 447 TYR 0.012 0.001 TYR 5 42 ARG 0.004 0.000 ARG 6 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 352 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue SER 403 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 674 MET cc_start: 0.9554 (mmm) cc_final: 0.9166 (mmp) REVERT: 2 793 MET cc_start: 0.8569 (mmp) cc_final: 0.8221 (mmp) REVERT: 3 398 MET cc_start: 0.9303 (mmm) cc_final: 0.9082 (mmm) REVERT: 4 351 MET cc_start: 0.8434 (tmm) cc_final: 0.8193 (tmm) REVERT: 4 684 MET cc_start: 0.9208 (ptm) cc_final: 0.8803 (ppp) REVERT: 5 445 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8867 (m-30) REVERT: 6 445 GLU cc_start: 0.8439 (tt0) cc_final: 0.7759 (tm-30) REVERT: 7 109 MET cc_start: 0.9275 (mmm) cc_final: 0.8992 (ttt) REVERT: 7 430 GLU cc_start: 0.8833 (tt0) cc_final: 0.8343 (pp20) REVERT: 7 438 ASP cc_start: 0.8565 (t0) cc_final: 0.7928 (t0) outliers start: 16 outliers final: 10 residues processed: 163 average time/residue: 0.8613 time to fit residues: 215.9677 Evaluate side-chains 159 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 332 CYS Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 3 residue 13 ARG Chi-restraints excluded: chain 3 residue 502 LEU Chi-restraints excluded: chain 4 residue 361 MET Chi-restraints excluded: chain 4 residue 368 HIS Chi-restraints excluded: chain 4 residue 757 ASP Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 6 residue 202 ASP Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 7 residue 102 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 60 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 160 optimal weight: 0.0970 chunk 317 optimal weight: 0.4980 chunk 271 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 328 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 593 ASN ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.056011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.044304 restraints weight = 698298.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.046199 restraints weight = 295981.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.047365 restraints weight = 179991.263| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28831 Z= 0.216 Angle : 0.481 6.535 38910 Z= 0.250 Chirality : 0.038 0.141 4422 Planarity : 0.003 0.047 5007 Dihedral : 6.143 86.369 4039 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.80 % Allowed : 7.96 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3481 helix: 2.15 (0.14), residues: 1474 sheet: -1.05 (0.19), residues: 753 loop : -0.70 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 6 334 HIS 0.005 0.001 HIS 2 686 PHE 0.012 0.001 PHE 5 447 TYR 0.013 0.001 TYR 5 42 ARG 0.004 0.000 ARG 5 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 352 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue SER 403 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 674 MET cc_start: 0.9562 (mmm) cc_final: 0.9169 (mmp) REVERT: 2 793 MET cc_start: 0.8586 (mmp) cc_final: 0.8211 (mmp) REVERT: 3 369 THR cc_start: 0.9565 (OUTLIER) cc_final: 0.9257 (t) REVERT: 4 351 MET cc_start: 0.8459 (tmm) cc_final: 0.8221 (tmm) REVERT: 4 684 MET cc_start: 0.9187 (ptm) cc_final: 0.8797 (ppp) REVERT: 5 445 ASP cc_start: 0.9155 (OUTLIER) cc_final: 0.8877 (m-30) REVERT: 6 445 GLU cc_start: 0.8405 (tt0) cc_final: 0.7719 (tm-30) REVERT: 7 109 MET cc_start: 0.9273 (mmm) cc_final: 0.9003 (ttt) REVERT: 7 306 MET cc_start: 0.7891 (mtm) cc_final: 0.7361 (mtm) REVERT: 7 430 GLU cc_start: 0.8815 (tt0) cc_final: 0.8320 (pp20) REVERT: 7 438 ASP cc_start: 0.8568 (t0) cc_final: 0.7941 (t0) outliers start: 25 outliers final: 16 residues processed: 169 average time/residue: 0.8496 time to fit residues: 223.9834 Evaluate side-chains 162 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 3.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 332 CYS Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 3 residue 13 ARG Chi-restraints excluded: chain 3 residue 111 VAL Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 3 residue 471 LEU Chi-restraints excluded: chain 3 residue 502 LEU Chi-restraints excluded: chain 3 residue 626 THR Chi-restraints excluded: chain 4 residue 361 MET Chi-restraints excluded: chain 4 residue 368 HIS Chi-restraints excluded: chain 4 residue 533 THR Chi-restraints excluded: chain 4 residue 712 GLU Chi-restraints excluded: chain 4 residue 757 ASP Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 6 residue 202 ASP Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 7 residue 102 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 68 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 306 optimal weight: 0.2980 chunk 333 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.053190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.041009 restraints weight = 553262.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.042722 restraints weight = 225632.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.043837 restraints weight = 131417.383| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28831 Z= 0.241 Angle : 0.487 7.046 38910 Z= 0.254 Chirality : 0.038 0.139 4422 Planarity : 0.003 0.049 5007 Dihedral : 6.139 89.732 4039 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.80 % Allowed : 8.50 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3481 helix: 2.12 (0.14), residues: 1476 sheet: -1.04 (0.19), residues: 760 loop : -0.76 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 6 334 HIS 0.004 0.001 HIS 2 686 PHE 0.012 0.001 PHE 5 393 TYR 0.014 0.001 TYR 5 42 ARG 0.004 0.000 ARG 7 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 352 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue SER 403 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 4.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 674 MET cc_start: 0.9558 (mmm) cc_final: 0.9153 (mmp) REVERT: 2 793 MET cc_start: 0.8586 (mmp) cc_final: 0.8198 (mmp) REVERT: 3 369 THR cc_start: 0.9527 (OUTLIER) cc_final: 0.9194 (t) REVERT: 4 684 MET cc_start: 0.9165 (ptm) cc_final: 0.8781 (ppp) REVERT: 5 128 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9111 (pp) REVERT: 5 445 ASP cc_start: 0.9265 (OUTLIER) cc_final: 0.8870 (m-30) REVERT: 6 445 GLU cc_start: 0.8437 (tt0) cc_final: 0.7711 (tm-30) REVERT: 7 109 MET cc_start: 0.9254 (mmm) cc_final: 0.8978 (ttt) REVERT: 7 430 GLU cc_start: 0.8889 (tt0) cc_final: 0.8331 (pp20) REVERT: 7 438 ASP cc_start: 0.8685 (t0) cc_final: 0.8059 (t0) REVERT: 7 621 MET cc_start: 0.9172 (mmt) cc_final: 0.8766 (mmm) outliers start: 25 outliers final: 18 residues processed: 168 average time/residue: 0.8914 time to fit residues: 236.0604 Evaluate side-chains 163 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 3.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 332 CYS Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 3 residue 111 VAL Chi-restraints excluded: chain 3 residue 334 HIS Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 3 residue 471 LEU Chi-restraints excluded: chain 3 residue 502 LEU Chi-restraints excluded: chain 3 residue 626 THR Chi-restraints excluded: chain 4 residue 202 VAL Chi-restraints excluded: chain 4 residue 368 HIS Chi-restraints excluded: chain 4 residue 533 THR Chi-restraints excluded: chain 4 residue 712 GLU Chi-restraints excluded: chain 4 residue 757 ASP Chi-restraints excluded: chain 5 residue 128 LEU Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 6 residue 202 ASP Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 613 SER Chi-restraints excluded: chain 7 residue 102 TYR Chi-restraints excluded: chain 7 residue 347 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 348 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 288 optimal weight: 9.9990 chunk 275 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 464 GLN 6 581 GLN ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.053069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.040907 restraints weight = 556751.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.042605 restraints weight = 226382.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.043706 restraints weight = 131714.637| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 28831 Z= 0.347 Angle : 0.536 7.325 38910 Z= 0.285 Chirality : 0.039 0.141 4422 Planarity : 0.003 0.049 5007 Dihedral : 6.234 87.929 4039 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.93 % Allowed : 8.79 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3481 helix: 1.84 (0.13), residues: 1474 sheet: -1.10 (0.19), residues: 731 loop : -0.91 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 6 334 HIS 0.013 0.001 HIS 7 347 PHE 0.012 0.001 PHE 6 412 TYR 0.017 0.001 TYR 5 42 ARG 0.005 0.000 ARG 6 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 352 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue SER 403 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 674 MET cc_start: 0.9577 (mmm) cc_final: 0.9169 (mmp) REVERT: 2 793 MET cc_start: 0.8619 (mmp) cc_final: 0.8231 (mmp) REVERT: 3 369 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9219 (t) REVERT: 4 684 MET cc_start: 0.9217 (ptm) cc_final: 0.8803 (ppp) REVERT: 5 128 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9186 (pp) REVERT: 5 445 ASP cc_start: 0.9319 (OUTLIER) cc_final: 0.9028 (m-30) REVERT: 6 445 GLU cc_start: 0.8477 (tt0) cc_final: 0.7696 (tm-30) REVERT: 7 109 MET cc_start: 0.9289 (mmm) cc_final: 0.9004 (ttt) REVERT: 7 430 GLU cc_start: 0.8936 (tt0) cc_final: 0.8331 (pp20) REVERT: 7 438 ASP cc_start: 0.8899 (t0) cc_final: 0.8292 (t0) REVERT: 7 621 MET cc_start: 0.9168 (mmt) cc_final: 0.8772 (mmm) outliers start: 29 outliers final: 23 residues processed: 170 average time/residue: 0.8222 time to fit residues: 217.6908 Evaluate side-chains 168 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 332 CYS Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 3 residue 13 ARG Chi-restraints excluded: chain 3 residue 111 VAL Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 334 HIS Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 3 residue 471 LEU Chi-restraints excluded: chain 3 residue 502 LEU Chi-restraints excluded: chain 3 residue 626 THR Chi-restraints excluded: chain 4 residue 202 VAL Chi-restraints excluded: chain 4 residue 354 LEU Chi-restraints excluded: chain 4 residue 368 HIS Chi-restraints excluded: chain 4 residue 533 THR Chi-restraints excluded: chain 4 residue 712 GLU Chi-restraints excluded: chain 4 residue 757 ASP Chi-restraints excluded: chain 5 residue 128 LEU Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 6 residue 202 ASP Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 613 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 102 TYR Chi-restraints excluded: chain 7 residue 380 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 120 optimal weight: 7.9990 chunk 350 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 331 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 771 GLN 6 404 GLN ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.052549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.040587 restraints weight = 550381.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.042263 restraints weight = 226052.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.043344 restraints weight = 132024.702| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28831 Z= 0.282 Angle : 0.514 8.685 38910 Z= 0.270 Chirality : 0.039 0.140 4422 Planarity : 0.003 0.051 5007 Dihedral : 6.174 78.187 4039 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.03 % Allowed : 8.76 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3481 helix: 1.86 (0.14), residues: 1474 sheet: -1.15 (0.19), residues: 731 loop : -0.90 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 6 334 HIS 0.004 0.001 HIS 2 686 PHE 0.012 0.001 PHE 5 393 TYR 0.015 0.001 TYR 5 42 ARG 0.004 0.000 ARG 2 664 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 352 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue SER 403 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 674 MET cc_start: 0.9574 (mmm) cc_final: 0.9168 (mmp) REVERT: 2 793 MET cc_start: 0.8655 (mmp) cc_final: 0.8260 (mmp) REVERT: 3 369 THR cc_start: 0.9546 (OUTLIER) cc_final: 0.9229 (t) REVERT: 4 337 MET cc_start: 0.8739 (mmm) cc_final: 0.8222 (mmm) REVERT: 4 684 MET cc_start: 0.9199 (ptm) cc_final: 0.8792 (ppp) REVERT: 5 128 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9177 (pp) REVERT: 5 445 ASP cc_start: 0.9306 (OUTLIER) cc_final: 0.9033 (m-30) REVERT: 6 445 GLU cc_start: 0.8475 (tt0) cc_final: 0.7734 (tm-30) REVERT: 7 430 GLU cc_start: 0.8924 (tt0) cc_final: 0.8398 (pp20) REVERT: 7 621 MET cc_start: 0.9164 (mmt) cc_final: 0.8774 (mmm) outliers start: 32 outliers final: 23 residues processed: 168 average time/residue: 0.8203 time to fit residues: 216.4982 Evaluate side-chains 164 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 332 CYS Chi-restraints excluded: chain 2 residue 592 MET Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 3 residue 111 VAL Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 334 HIS Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 3 residue 466 MET Chi-restraints excluded: chain 3 residue 471 LEU Chi-restraints excluded: chain 3 residue 502 LEU Chi-restraints excluded: chain 3 residue 626 THR Chi-restraints excluded: chain 4 residue 202 VAL Chi-restraints excluded: chain 4 residue 354 LEU Chi-restraints excluded: chain 4 residue 368 HIS Chi-restraints excluded: chain 4 residue 533 THR Chi-restraints excluded: chain 4 residue 712 GLU Chi-restraints excluded: chain 4 residue 757 ASP Chi-restraints excluded: chain 5 residue 128 LEU Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 6 residue 202 ASP Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 613 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 102 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 204 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 318 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.053255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.040587 restraints weight = 568780.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.042308 restraints weight = 236125.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.043448 restraints weight = 139709.911| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28831 Z= 0.183 Angle : 0.483 9.531 38910 Z= 0.248 Chirality : 0.039 0.142 4422 Planarity : 0.003 0.053 5007 Dihedral : 6.050 87.398 4039 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.90 % Allowed : 8.92 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3481 helix: 2.08 (0.14), residues: 1484 sheet: -1.06 (0.19), residues: 733 loop : -0.83 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 6 334 HIS 0.005 0.001 HIS 2 686 PHE 0.012 0.001 PHE 5 393 TYR 0.012 0.001 TYR 5 42 ARG 0.005 0.000 ARG 2 664 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 352 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue SER 403 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 674 MET cc_start: 0.9579 (mmm) cc_final: 0.9180 (mmp) REVERT: 2 793 MET cc_start: 0.8682 (mmp) cc_final: 0.8276 (mmp) REVERT: 3 268 MET cc_start: 0.8615 (ptp) cc_final: 0.8275 (ptp) REVERT: 3 369 THR cc_start: 0.9532 (OUTLIER) cc_final: 0.9220 (t) REVERT: 4 337 MET cc_start: 0.8737 (mmm) cc_final: 0.8256 (mmm) REVERT: 4 684 MET cc_start: 0.9235 (ptm) cc_final: 0.8837 (ppp) REVERT: 5 128 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9187 (pp) REVERT: 5 445 ASP cc_start: 0.9305 (OUTLIER) cc_final: 0.9021 (m-30) REVERT: 6 445 GLU cc_start: 0.8456 (tt0) cc_final: 0.7730 (tm-30) REVERT: 7 438 ASP cc_start: 0.8766 (t0) cc_final: 0.8144 (t0) REVERT: 7 621 MET cc_start: 0.9177 (mmt) cc_final: 0.8804 (mmm) outliers start: 28 outliers final: 21 residues processed: 164 average time/residue: 0.8641 time to fit residues: 224.6881 Evaluate side-chains 164 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 332 CYS Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 3 residue 111 VAL Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 334 HIS Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 3 residue 466 MET Chi-restraints excluded: chain 3 residue 471 LEU Chi-restraints excluded: chain 3 residue 502 LEU Chi-restraints excluded: chain 3 residue 626 THR Chi-restraints excluded: chain 4 residue 202 VAL Chi-restraints excluded: chain 4 residue 368 HIS Chi-restraints excluded: chain 4 residue 533 THR Chi-restraints excluded: chain 4 residue 757 ASP Chi-restraints excluded: chain 5 residue 74 MET Chi-restraints excluded: chain 5 residue 128 LEU Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 6 residue 202 ASP Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 613 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 125 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 264 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.055696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.044045 restraints weight = 697406.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.045917 restraints weight = 296024.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.047075 restraints weight = 180158.304| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28831 Z= 0.195 Angle : 0.487 9.727 38910 Z= 0.251 Chirality : 0.039 0.229 4422 Planarity : 0.003 0.055 5007 Dihedral : 6.015 89.850 4039 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.83 % Allowed : 9.02 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3481 helix: 2.14 (0.14), residues: 1483 sheet: -1.06 (0.19), residues: 733 loop : -0.78 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 6 334 HIS 0.004 0.001 HIS 2 686 PHE 0.012 0.001 PHE 5 393 TYR 0.013 0.001 TYR 5 42 ARG 0.004 0.000 ARG 2 664 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 352 is missing expected H atoms. Skipping. Residue SER 517 is missing expected H atoms. Skipping. Residue SER 403 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 3.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 674 MET cc_start: 0.9577 (mmm) cc_final: 0.9173 (mmp) REVERT: 2 793 MET cc_start: 0.8673 (mmp) cc_final: 0.8346 (mmp) REVERT: 3 369 THR cc_start: 0.9589 (OUTLIER) cc_final: 0.9314 (t) REVERT: 4 337 MET cc_start: 0.8696 (mmm) cc_final: 0.8210 (mmm) REVERT: 4 684 MET cc_start: 0.9207 (ptm) cc_final: 0.8826 (ppp) REVERT: 5 445 ASP cc_start: 0.9175 (OUTLIER) cc_final: 0.8885 (m-30) REVERT: 6 340 MET cc_start: 0.9029 (mmm) cc_final: 0.8803 (mmm) REVERT: 6 445 GLU cc_start: 0.8403 (tt0) cc_final: 0.7778 (tm-30) REVERT: 7 438 ASP cc_start: 0.8691 (t0) cc_final: 0.8082 (t0) REVERT: 7 621 MET cc_start: 0.9158 (mmt) cc_final: 0.8772 (mmm) outliers start: 26 outliers final: 21 residues processed: 161 average time/residue: 0.8478 time to fit residues: 216.5024 Evaluate side-chains 161 residues out of total 3116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 332 CYS Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 3 residue 111 VAL Chi-restraints excluded: chain 3 residue 237 VAL Chi-restraints excluded: chain 3 residue 334 HIS Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 3 residue 466 MET Chi-restraints excluded: chain 3 residue 471 LEU Chi-restraints excluded: chain 3 residue 502 LEU Chi-restraints excluded: chain 3 residue 626 THR Chi-restraints excluded: chain 4 residue 202 VAL Chi-restraints excluded: chain 4 residue 368 HIS Chi-restraints excluded: chain 4 residue 533 THR Chi-restraints excluded: chain 4 residue 757 ASP Chi-restraints excluded: chain 5 residue 74 MET Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 6 residue 202 ASP Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 613 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 243 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 254 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.053487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.040783 restraints weight = 581084.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.042524 restraints weight = 242307.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.043665 restraints weight = 142991.845| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28831 Z= 0.291 Angle : 0.520 9.388 38910 Z= 0.272 Chirality : 0.038 0.139 4422 Planarity : 0.003 0.054 5007 Dihedral : 6.092 84.733 4039 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.80 % Allowed : 9.24 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3481 helix: 1.96 (0.13), residues: 1484 sheet: -1.13 (0.19), residues: 731 loop : -0.88 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 6 334 HIS 0.005 0.001 HIS 3 196 PHE 0.013 0.001 PHE 5 393 TYR 0.016 0.001 TYR 5 42 ARG 0.004 0.000 ARG 6 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13756.70 seconds wall clock time: 237 minutes 22.96 seconds (14242.96 seconds total)