Starting phenix.real_space_refine on Sat Sep 12 18:59:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7re2_24431/09_2026/7re2_24431.cif Found real_map, /net/cci-nas-00/data/ceres_data/7re2_24431/09_2026/7re2_24431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7re2_24431/09_2026/7re2_24431.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7re2_24431/09_2026/7re2_24431.cif" model { file = "/net/cci-nas-00/data/ceres_data/7re2_24431/09_2026/7re2_24431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7re2_24431/09_2026/7re2_24431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7re2_24431/09_2026/7re2_24431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7re2_24431/09_2026/7re2_24431.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.099 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: 9 Type Number sf(0) Gaussians Zn 5 6.06 5 Al 1 5.89 5 P 75 5.49 5 Mg 2 5.21 5 S 117 5.16 5 C 10578 2.51 5 N 2881 2.21 5 O 3434 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17096 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1415 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4557 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNAv2': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNAv2': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 85.918 102.516 109.737 1.00 38.59 S ATOM 2495 SG CYS A 306 86.531 101.117 113.281 1.00 34.60 S ATOM 2527 SG CYS A 310 84.787 104.460 112.792 1.00 36.67 S ATOM 3935 SG CYS A 487 84.393 87.754 95.382 1.00 37.43 S ATOM 5188 SG CYS A 645 85.593 86.047 98.607 1.00 43.02 S ATOM 5194 SG CYS A 646 86.107 89.800 98.006 1.00 40.03 S ATOM 10896 SG CYS E 5 37.457 84.570 46.824 1.00 79.46 S ATOM 10917 SG CYS E 8 35.387 83.599 48.135 1.00 83.51 S ATOM 11055 SG CYS E 26 36.939 80.207 47.399 1.00 82.68 S ATOM 11076 SG CYS E 29 35.959 82.112 44.541 1.00 87.27 S ATOM 11241 SG CYS E 50 59.124 68.782 43.616 1.00116.45 S ATOM 11271 SG CYS E 55 60.774 69.332 40.436 1.00119.99 S ATOM 11404 SG CYS E 72 58.262 66.287 40.676 1.00122.40 S ATOM 10978 SG CYS E 16 47.202 83.633 40.362 1.00 93.01 S ATOM 10993 SG CYS E 19 46.267 87.298 39.423 1.00100.24 S Time building chain proxies: 3.47, per 1000 atoms: 0.20 Number of scatterers: 17096 At special positions: 0 Unit cell: (104.86, 154.08, 174.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 5 29.99 S 117 16.00 P 75 15.00 Al 1 13.00 Mg 2 11.99 F 3 9.00 O 3434 8.00 N 2881 7.00 C 10578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 707.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " Number of angles added : 16 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3758 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 21 sheets defined 49.8% alpha, 12.6% beta 34 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.696A pdb=" N PHE A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.601A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 removed outlier: 3.741A pdb=" N LEU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 4.021A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.872A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.586A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.931A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.531A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.768A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.977A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.536A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.044A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.611A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.246A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 removed outlier: 3.591A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.414A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.927A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 98 removed outlier: 3.948A pdb=" N MET B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.958A pdb=" N ASP B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.517A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.541A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.632A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.593A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 32 through 82 Processing helix chain 'D' and resid 83 through 99 removed outlier: 3.700A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.701A pdb=" N ILE D 172 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 93 through 97 removed outlier: 3.627A pdb=" N THR E 96 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N CYS E 97 " --> pdb=" O LYS E 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 97' Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.592A pdb=" N PHE E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.289A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 145 Processing helix chain 'E' and resid 146 through 149 Processing helix chain 'E' and resid 262 through 264 No H-bonds generated for 'chain 'E' and resid 262 through 264' Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'E' and resid 287 through 299 removed outlier: 4.013A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 325 Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 376 through 379 Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 removed outlier: 3.718A pdb=" N ILE E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 453 Processing helix chain 'E' and resid 489 through 499 Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.866A pdb=" N ARG E 507 " --> pdb=" O PRO E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 527 removed outlier: 4.232A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE E 525 " --> pdb=" O VAL E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 537 Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 578 through 585 removed outlier: 4.064A pdb=" N LEU E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.102A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP A 60 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 66 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.316A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.141A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 339 removed outlier: 6.500A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 560 removed outlier: 3.501A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 758 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.361A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.361A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB4, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.768A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AB7, first strand: chain 'E' and resid 166 through 167 removed outlier: 3.552A pdb=" N ALA E 152 " --> pdb=" O PHE E 225 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG E 212 " --> pdb=" O THR E 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 162 through 164 Processing sheet with id=AB9, first strand: chain 'E' and resid 356 through 359 removed outlier: 3.739A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 366 through 368 removed outlier: 6.470A pdb=" N THR E 366 " --> pdb=" O ARG E 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 471 through 475 removed outlier: 6.998A pdb=" N ASP E 542 " --> pdb=" O LYS E 569 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY E 571 " --> pdb=" O ASP E 542 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL E 544 " --> pdb=" O GLY E 571 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 481 through 482 765 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4780 1.33 - 1.45: 3334 1.45 - 1.57: 9123 1.57 - 1.69: 197 1.69 - 1.81: 175 Bond restraints: 17609 Sorted by residual: bond pdb=" F2 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" F1 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" F3 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" C17 1N7 A1005 " pdb=" C18 1N7 A1005 " ideal model delta sigma weight residual 1.528 1.636 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C17 1N7 A1006 " pdb=" C18 1N7 A1006 " ideal model delta sigma weight residual 1.528 1.631 -0.103 2.00e-02 2.50e+03 2.65e+01 ... (remaining 17604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 23899 2.52 - 5.04: 326 5.04 - 7.56: 40 7.56 - 10.08: 6 10.08 - 12.60: 3 Bond angle restraints: 24274 Sorted by residual: angle pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta sigma weight residual 121.70 134.30 -12.60 1.80e+00 3.09e-01 4.90e+01 angle pdb=" N ILE E 432 " pdb=" CA ILE E 432 " pdb=" C ILE E 432 " ideal model delta sigma weight residual 113.47 109.50 3.97 1.01e+00 9.80e-01 1.54e+01 angle pdb=" C4 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C9 1N7 A1005 " ideal model delta sigma weight residual 117.60 105.93 11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" N LYS E 189 " pdb=" CA LYS E 189 " pdb=" C LYS E 189 " ideal model delta sigma weight residual 110.80 118.73 -7.93 2.13e+00 2.20e-01 1.39e+01 ... (remaining 24269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 10130 35.83 - 71.65: 198 71.65 - 107.48: 13 107.48 - 143.30: 3 143.30 - 179.13: 4 Dihedral angle restraints: 10348 sinusoidal: 4529 harmonic: 5819 Sorted by residual: dihedral pdb=" C4' A P 35 " pdb=" C3' A P 35 " pdb=" C2' A P 35 " pdb=" C1' A P 35 " ideal model delta sinusoidal sigma weight residual 36.34 -35.50 71.85 1 3.10e+00 1.04e-01 6.88e+02 dihedral pdb=" O4' A P 35 " pdb=" C4' A P 35 " pdb=" C3' A P 35 " pdb=" C2' A P 35 " ideal model delta sinusoidal sigma weight residual -35.15 23.03 -58.17 1 4.00e+00 6.25e-02 2.84e+02 dihedral pdb=" O4' A P 35 " pdb=" C2' A P 35 " pdb=" C1' A P 35 " pdb=" C3' A P 35 " ideal model delta sinusoidal sigma weight residual -94.41 -36.72 -57.69 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 10345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.028: 2828 1.028 - 2.055: 0 2.055 - 3.083: 0 3.083 - 4.110: 0 4.110 - 5.138: 2 Chirality restraints: 2830 Sorted by residual: chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.71 -5.14 2.00e-01 2.50e+01 6.60e+02 chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.59 5.12 2.00e-01 2.50e+01 6.56e+02 chirality pdb=" C17 1N7 A1006 " pdb=" C16 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" O3 1N7 A1006 " both_signs ideal model delta sigma weight residual False 2.40 2.81 -0.41 2.00e-01 2.50e+01 4.23e+00 ... (remaining 2827 not shown) Planarity restraints: 2811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 132 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO D 133 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 133 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 133 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 231 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 232 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 927 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " 0.017 5.00e-02 4.00e+02 ... (remaining 2808 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 117 2.53 - 3.12: 12891 3.12 - 3.71: 27451 3.71 - 4.31: 38357 4.31 - 4.90: 63303 Nonbonded interactions: 142119 Sorted by model distance: nonbonded pdb="MG MG A1003 " pdb=" O1A ADP A1004 " model vdw 1.932 2.170 nonbonded pdb=" O3B ADP E 704 " pdb="MG MG E 705 " model vdw 1.994 2.170 nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1003 " model vdw 2.003 2.170 nonbonded pdb=" OG SER E 289 " pdb="MG MG E 705 " model vdw 2.039 2.170 nonbonded pdb=" OD2 ASP A 218 " pdb="MG MG A1003 " model vdw 2.048 2.170 ... (remaining 142114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 7 through 22 or (resid 23 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 through 191)) selection = (chain 'D' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thro \ ugh 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.900 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 0.010 0.877 17630 Z= 0.732 Angle : 0.791 40.155 24290 Z= 0.349 Chirality : 0.149 5.138 2830 Planarity : 0.003 0.038 2811 Dihedral : 13.748 179.128 6590 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.42 % Allowed : 7.62 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1953 helix: 0.72 (0.18), residues: 848 sheet: -0.99 (0.34), residues: 223 loop : -1.26 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.016 0.001 TYR A 788 PHE 0.016 0.002 PHE A 741 TRP 0.015 0.001 TRP A 916 HIS 0.008 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.31 (17609) covalent geometry : angle 0.69170 / 0.34 (24274) hydrogen bonds : bond 0.16837 / 11.56 ( 840) hydrogen bonds : angle 6.11951 / 4.33 ( 2277) metal coordination : bond 0.06658 / 3.88 ( 20) metal coordination : angle 14.93358 / 8.66 ( 16) Misc. bond : bond 0.87742 / 46.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 221 ASP cc_start: 0.7776 (p0) cc_final: 0.7570 (p0) REVERT: A 258 ASP cc_start: 0.7065 (t0) cc_final: 0.6801 (t0) REVERT: D 70 MET cc_start: 0.7958 (tpt) cc_final: 0.7752 (tpt) outliers start: 41 outliers final: 25 residues processed: 217 average time/residue: 0.1462 time to fit residues: 47.4595 Evaluate side-chains 180 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 562 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.156297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.106385 restraints weight = 25526.649| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.04 r_work: 0.3107 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17630 Z= 0.159 Angle : 0.612 14.844 24290 Z= 0.293 Chirality : 0.044 0.345 2830 Planarity : 0.004 0.036 2811 Dihedral : 11.164 175.653 3068 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.77 % Allowed : 10.09 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 1953 helix: 0.85 (0.18), residues: 871 sheet: -0.72 (0.36), residues: 201 loop : -1.15 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 443 TYR 0.017 0.001 TYR D 138 PHE 0.016 0.002 PHE E 422 TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (17609) covalent geometry : angle 0.59553 / 0.29 (24274) hydrogen bonds : bond 0.04146 / 2.81 ( 840) hydrogen bonds : angle 4.56486 / 3.19 ( 2277) metal coordination : bond 0.01019 / 0.52 ( 20) metal coordination : angle 5.45431 / 2.97 ( 16) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.615 Fit side-chains REVERT: A 10 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7929 (tpt90) REVERT: A 105 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7881 (ttm-80) REVERT: A 110 MET cc_start: 0.8345 (mmm) cc_final: 0.8024 (mmm) REVERT: A 221 ASP cc_start: 0.8529 (p0) cc_final: 0.8176 (p0) REVERT: A 258 ASP cc_start: 0.8117 (t0) cc_final: 0.7772 (t0) REVERT: B 43 ASN cc_start: 0.7433 (m-40) cc_final: 0.7156 (t0) REVERT: B 104 ASN cc_start: 0.8355 (m-40) cc_final: 0.7834 (m110) REVERT: C 34 GLN cc_start: 0.8637 (tp40) cc_final: 0.7979 (tm-30) REVERT: D 38 LEU cc_start: 0.7169 (mt) cc_final: 0.6805 (tt) REVERT: E 378 MET cc_start: 0.6744 (ttm) cc_final: 0.6534 (ttm) outliers start: 47 outliers final: 32 residues processed: 203 average time/residue: 0.1384 time to fit residues: 42.5817 Evaluate side-chains 185 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 159 optimal weight: 0.0570 chunk 42 optimal weight: 0.0570 chunk 140 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 189 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN B 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.157423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105554 restraints weight = 25583.542| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.05 r_work: 0.3151 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17630 Z= 0.132 Angle : 0.574 12.643 24290 Z= 0.272 Chirality : 0.043 0.332 2830 Planarity : 0.003 0.033 2811 Dihedral : 10.736 171.954 3058 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.95 % Allowed : 11.16 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.19), residues: 1953 helix: 1.01 (0.18), residues: 872 sheet: -0.57 (0.35), residues: 196 loop : -1.01 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 51 TYR 0.013 0.001 TYR D 138 PHE 0.014 0.001 PHE A 652 TRP 0.012 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (17609) covalent geometry : angle 0.56138 / 0.27 (24274) hydrogen bonds : bond 0.03624 / 2.45 ( 840) hydrogen bonds : angle 4.29602 / 3.00 ( 2277) metal coordination : bond 0.00685 / 0.37 ( 20) metal coordination : angle 4.62821 / 2.53 ( 16) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7889 (tpt90) REVERT: A 98 LYS cc_start: 0.8344 (tptt) cc_final: 0.8052 (mmmt) REVERT: A 221 ASP cc_start: 0.8575 (p0) cc_final: 0.8204 (p0) REVERT: A 258 ASP cc_start: 0.8077 (t0) cc_final: 0.7741 (t0) REVERT: A 260 ASP cc_start: 0.8466 (t0) cc_final: 0.8260 (t0) REVERT: A 626 MET cc_start: 0.9116 (ttm) cc_final: 0.8899 (ttm) REVERT: A 665 GLU cc_start: 0.8316 (pm20) cc_final: 0.7628 (pm20) REVERT: B 43 ASN cc_start: 0.7491 (m-40) cc_final: 0.7242 (t0) REVERT: B 104 ASN cc_start: 0.8263 (m-40) cc_final: 0.7809 (m-40) REVERT: C 34 GLN cc_start: 0.8573 (tp40) cc_final: 0.7898 (tm-30) REVERT: D 38 LEU cc_start: 0.7197 (mt) cc_final: 0.6853 (tt) REVERT: E 376 ILE cc_start: 0.5526 (OUTLIER) cc_final: 0.5267 (pp) REVERT: E 378 MET cc_start: 0.6680 (ttm) cc_final: 0.6457 (ttm) REVERT: E 543 TYR cc_start: 0.4831 (m-80) cc_final: 0.4592 (m-80) outliers start: 50 outliers final: 34 residues processed: 210 average time/residue: 0.1457 time to fit residues: 45.9892 Evaluate side-chains 190 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 84 optimal weight: 0.0980 chunk 109 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 48 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 overall best weight: 2.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN E 464 HIS E 470 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.155247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.103981 restraints weight = 25522.718| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.89 r_work: 0.3134 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17630 Z= 0.212 Angle : 0.611 12.734 24290 Z= 0.295 Chirality : 0.045 0.345 2830 Planarity : 0.003 0.036 2811 Dihedral : 10.670 175.497 3054 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.42 % Allowed : 12.04 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 1953 helix: 0.94 (0.18), residues: 873 sheet: -0.65 (0.35), residues: 208 loop : -1.03 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.015 0.001 TYR A 788 PHE 0.017 0.002 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.008 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (17609) covalent geometry : angle 0.60205 / 0.29 (24274) hydrogen bonds : bond 0.03972 / 2.68 ( 840) hydrogen bonds : angle 4.33134 / 3.02 ( 2277) metal coordination : bond 0.00937 / 0.57 ( 20) metal coordination : angle 4.18630 / 2.29 ( 16) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 110 MET cc_start: 0.8334 (mmm) cc_final: 0.8071 (mmm) REVERT: A 221 ASP cc_start: 0.8664 (p0) cc_final: 0.8272 (p0) REVERT: A 258 ASP cc_start: 0.8082 (t0) cc_final: 0.7770 (t0) REVERT: A 260 ASP cc_start: 0.8503 (t0) cc_final: 0.8294 (t0) REVERT: B 43 ASN cc_start: 0.7546 (m-40) cc_final: 0.7130 (t0) REVERT: B 104 ASN cc_start: 0.8285 (m-40) cc_final: 0.7894 (m-40) REVERT: E 376 ILE cc_start: 0.5698 (OUTLIER) cc_final: 0.5362 (pp) REVERT: E 378 MET cc_start: 0.6754 (ttm) cc_final: 0.6478 (ttm) REVERT: E 543 TYR cc_start: 0.5206 (m-80) cc_final: 0.4914 (m-80) outliers start: 58 outliers final: 40 residues processed: 215 average time/residue: 0.1460 time to fit residues: 47.1492 Evaluate side-chains 202 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 194 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.156137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.104162 restraints weight = 25379.974| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.00 r_work: 0.3128 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17630 Z= 0.169 Angle : 0.585 12.747 24290 Z= 0.281 Chirality : 0.044 0.341 2830 Planarity : 0.003 0.038 2811 Dihedral : 10.522 179.087 3053 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.95 % Allowed : 13.75 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 1953 helix: 1.02 (0.18), residues: 876 sheet: -0.60 (0.34), residues: 213 loop : -1.00 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.013 0.001 TYR A 788 PHE 0.016 0.001 PHE A 652 TRP 0.012 0.001 TRP A 916 HIS 0.010 0.001 HIS E 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (17609) covalent geometry : angle 0.57636 / 0.28 (24274) hydrogen bonds : bond 0.03686 / 2.48 ( 840) hydrogen bonds : angle 4.24412 / 2.97 ( 2277) metal coordination : bond 0.00771 / 0.47 ( 20) metal coordination : angle 3.85513 / 2.10 ( 16) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: A 221 ASP cc_start: 0.8675 (p0) cc_final: 0.8271 (p0) REVERT: A 258 ASP cc_start: 0.8134 (t0) cc_final: 0.7812 (t0) REVERT: A 431 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7011 (mt-10) REVERT: A 626 MET cc_start: 0.9098 (ttm) cc_final: 0.8884 (ttm) REVERT: B 43 ASN cc_start: 0.7632 (m-40) cc_final: 0.7217 (t0) REVERT: B 104 ASN cc_start: 0.8264 (m-40) cc_final: 0.7870 (m110) REVERT: C 34 GLN cc_start: 0.8596 (tp40) cc_final: 0.7999 (tm-30) REVERT: D 38 LEU cc_start: 0.7234 (mt) cc_final: 0.6813 (tp) REVERT: E 378 MET cc_start: 0.6788 (ttm) cc_final: 0.6497 (ttm) REVERT: E 543 TYR cc_start: 0.5342 (m-80) cc_final: 0.4961 (m-80) outliers start: 50 outliers final: 38 residues processed: 205 average time/residue: 0.1408 time to fit residues: 43.6683 Evaluate side-chains 200 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 116 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 131 optimal weight: 0.1980 chunk 81 optimal weight: 0.0170 chunk 32 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.158827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.106563 restraints weight = 25366.121| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.03 r_work: 0.3192 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17630 Z= 0.101 Angle : 0.554 12.728 24290 Z= 0.262 Chirality : 0.043 0.325 2830 Planarity : 0.003 0.038 2811 Dihedral : 10.211 173.586 3051 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.36 % Allowed : 15.05 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1953 helix: 1.25 (0.18), residues: 871 sheet: -0.24 (0.36), residues: 194 loop : -0.89 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.011 0.001 TYR D 138 PHE 0.019 0.001 PHE E 561 TRP 0.012 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (17609) covalent geometry : angle 0.54681 / 0.26 (24274) hydrogen bonds : bond 0.03149 / 2.11 ( 840) hydrogen bonds : angle 4.07224 / 2.85 ( 2277) metal coordination : bond 0.00482 / 0.26 ( 20) metal coordination : angle 3.59554 / 1.94 ( 16) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.551 Fit side-chains REVERT: A 98 LYS cc_start: 0.8374 (tptt) cc_final: 0.8077 (tptt) REVERT: A 221 ASP cc_start: 0.8495 (p0) cc_final: 0.8112 (p0) REVERT: A 258 ASP cc_start: 0.8120 (t0) cc_final: 0.7795 (t0) REVERT: A 665 GLU cc_start: 0.8256 (pm20) cc_final: 0.7726 (pm20) REVERT: B 90 MET cc_start: 0.8938 (ttp) cc_final: 0.8469 (ttp) REVERT: C 34 GLN cc_start: 0.8581 (tp40) cc_final: 0.7983 (tm-30) REVERT: E 378 MET cc_start: 0.6748 (ttm) cc_final: 0.6452 (ttm) REVERT: E 543 TYR cc_start: 0.5390 (m-80) cc_final: 0.4955 (m-80) outliers start: 40 outliers final: 32 residues processed: 200 average time/residue: 0.1366 time to fit residues: 41.3356 Evaluate side-chains 189 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 128 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 192 optimal weight: 30.0000 chunk 80 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN A 468 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.155554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.103442 restraints weight = 25230.292| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.96 r_work: 0.3123 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17630 Z= 0.207 Angle : 0.616 12.814 24290 Z= 0.294 Chirality : 0.045 0.341 2830 Planarity : 0.003 0.040 2811 Dihedral : 10.245 174.233 3049 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.77 % Allowed : 15.53 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 1953 helix: 1.05 (0.18), residues: 878 sheet: -0.31 (0.36), residues: 199 loop : -0.93 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.016 0.001 TYR D 138 PHE 0.018 0.002 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.009 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (17609) covalent geometry : angle 0.60852 / 0.29 (24274) hydrogen bonds : bond 0.03847 / 2.59 ( 840) hydrogen bonds : angle 4.21337 / 2.95 ( 2277) metal coordination : bond 0.00928 / 0.58 ( 20) metal coordination : angle 3.76624 / 2.07 ( 16) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: A 221 ASP cc_start: 0.8650 (p0) cc_final: 0.8237 (p0) REVERT: A 258 ASP cc_start: 0.8150 (t0) cc_final: 0.7815 (t0) REVERT: B 43 ASN cc_start: 0.7659 (m-40) cc_final: 0.7199 (t0) REVERT: B 61 LYS cc_start: 0.8349 (tppt) cc_final: 0.8119 (tppt) REVERT: B 104 ASN cc_start: 0.8258 (m-40) cc_final: 0.7857 (m110) REVERT: B 140 ASN cc_start: 0.8266 (m-40) cc_final: 0.7894 (m-40) REVERT: C 34 GLN cc_start: 0.8601 (tp40) cc_final: 0.7979 (tm-30) REVERT: D 38 LEU cc_start: 0.7277 (mt) cc_final: 0.6857 (tt) REVERT: E 378 MET cc_start: 0.6858 (ttm) cc_final: 0.6559 (ttm) REVERT: E 543 TYR cc_start: 0.5793 (m-80) cc_final: 0.5371 (m-80) REVERT: E 576 MET cc_start: 0.0865 (ptm) cc_final: 0.0459 (ptm) REVERT: E 582 TYR cc_start: 0.4307 (t80) cc_final: 0.3902 (t80) outliers start: 47 outliers final: 36 residues processed: 201 average time/residue: 0.1432 time to fit residues: 43.4389 Evaluate side-chains 197 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 71 optimal weight: 0.0470 chunk 115 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 143 optimal weight: 0.5980 chunk 128 optimal weight: 0.0970 chunk 156 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN ** E 404 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 = 0.4124 r_free = 0.4124 target = 0.159228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108147 restraints weight = 25310.178| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.53 r_work: 0.3171 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17630 Z= 0.098 Angle : 0.554 12.734 24290 Z= 0.261 Chirality : 0.043 0.323 2830 Planarity : 0.003 0.041 2811 Dihedral : 10.006 175.329 3049 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.36 % Allowed : 16.00 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1953 helix: 1.29 (0.18), residues: 878 sheet: -0.09 (0.37), residues: 188 loop : -0.80 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.012 0.001 TYR D 138 PHE 0.013 0.001 PHE A 652 TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (17609) covalent geometry : angle 0.54660 / 0.26 (24274) hydrogen bonds : bond 0.03081 / 2.07 ( 840) hydrogen bonds : angle 4.03660 / 2.82 ( 2277) metal coordination : bond 0.00400 / 0.22 ( 20) metal coordination : angle 3.56086 / 1.91 ( 16) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.682 Fit side-chains REVERT: A 98 LYS cc_start: 0.8485 (tptt) cc_final: 0.8096 (tppt) REVERT: A 110 MET cc_start: 0.8131 (mmm) cc_final: 0.7673 (tpp) REVERT: A 221 ASP cc_start: 0.8529 (p0) cc_final: 0.8138 (p0) REVERT: A 258 ASP cc_start: 0.8165 (t0) cc_final: 0.7836 (t0) REVERT: A 665 GLU cc_start: 0.8301 (pm20) cc_final: 0.7778 (pm20) REVERT: B 61 LYS cc_start: 0.8109 (tppt) cc_final: 0.7877 (tppt) REVERT: B 90 MET cc_start: 0.8906 (ttp) cc_final: 0.8446 (ttp) REVERT: C 34 GLN cc_start: 0.8562 (tp40) cc_final: 0.7932 (tm-30) REVERT: D 38 LEU cc_start: 0.7220 (mt) cc_final: 0.6788 (tt) REVERT: E 378 MET cc_start: 0.6724 (ttm) cc_final: 0.6411 (ttm) REVERT: E 543 TYR cc_start: 0.5778 (m-80) cc_final: 0.5320 (m-80) REVERT: E 576 MET cc_start: 0.0240 (ptm) cc_final: -0.0287 (ptm) REVERT: E 582 TYR cc_start: 0.4256 (t80) cc_final: 0.3806 (t80) outliers start: 40 outliers final: 32 residues processed: 203 average time/residue: 0.1393 time to fit residues: 42.8790 Evaluate side-chains 188 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 191 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.154202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103071 restraints weight = 25287.851| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.06 r_work: 0.3086 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 17630 Z= 0.291 Angle : 0.664 12.846 24290 Z= 0.320 Chirality : 0.047 0.347 2830 Planarity : 0.004 0.042 2811 Dihedral : 10.094 179.698 3046 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.60 % Allowed : 16.12 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1953 helix: 1.01 (0.18), residues: 873 sheet: -0.38 (0.36), residues: 202 loop : -0.94 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 51 TYR 0.019 0.002 TYR A 788 PHE 0.020 0.002 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.011 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.29 (17609) covalent geometry : angle 0.65693 / 0.32 (24274) hydrogen bonds : bond 0.04223 / 2.85 ( 840) hydrogen bonds : angle 4.30179 / 3.01 ( 2277) metal coordination : bond 0.01203 / 0.78 ( 20) metal coordination : angle 3.83821 / 2.13 ( 16) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8543 (tptt) cc_final: 0.8152 (tppt) REVERT: A 221 ASP cc_start: 0.8736 (p0) cc_final: 0.8312 (p0) REVERT: A 258 ASP cc_start: 0.8191 (t0) cc_final: 0.7862 (t0) REVERT: B 43 ASN cc_start: 0.7526 (m-40) cc_final: 0.7067 (t0) REVERT: B 59 LEU cc_start: 0.8286 (mm) cc_final: 0.7897 (tt) REVERT: B 61 LYS cc_start: 0.8300 (tppt) cc_final: 0.8042 (tppt) REVERT: B 104 ASN cc_start: 0.8286 (m-40) cc_final: 0.7927 (m110) REVERT: B 140 ASN cc_start: 0.8291 (m-40) cc_final: 0.7924 (m-40) REVERT: E 543 TYR cc_start: 0.5822 (m-80) cc_final: 0.5363 (m-80) outliers start: 44 outliers final: 37 residues processed: 196 average time/residue: 0.1449 time to fit residues: 42.6660 Evaluate side-chains 196 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 13 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 196 optimal weight: 8.9990 chunk 183 optimal weight: 30.0000 chunk 6 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.157877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.106135 restraints weight = 25153.839| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.48 r_work: 0.3144 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17630 Z= 0.115 Angle : 0.565 12.728 24290 Z= 0.269 Chirality : 0.043 0.332 2830 Planarity : 0.003 0.041 2811 Dihedral : 9.887 177.166 3046 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.18 % Allowed : 16.77 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 1953 helix: 1.20 (0.18), residues: 875 sheet: -0.19 (0.37), residues: 189 loop : -0.83 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 51 TYR 0.011 0.001 TYR A 515 PHE 0.014 0.001 PHE A 652 TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (17609) covalent geometry : angle 0.55795 / 0.27 (24274) hydrogen bonds : bond 0.03266 / 2.20 ( 840) hydrogen bonds : angle 4.09972 / 2.87 ( 2277) metal coordination : bond 0.00503 / 0.28 ( 20) metal coordination : angle 3.55525 / 1.92 ( 16) Misc. bond : bond 0.00041 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8472 (tptt) cc_final: 0.8093 (tppt) REVERT: A 110 MET cc_start: 0.8233 (mmm) cc_final: 0.7586 (tpp) REVERT: A 221 ASP cc_start: 0.8656 (p0) cc_final: 0.8237 (p0) REVERT: A 258 ASP cc_start: 0.8175 (t0) cc_final: 0.7865 (t0) REVERT: B 43 ASN cc_start: 0.7444 (m-40) cc_final: 0.7009 (t0) REVERT: B 59 LEU cc_start: 0.8204 (mm) cc_final: 0.7841 (tt) REVERT: B 61 LYS cc_start: 0.8126 (tppt) cc_final: 0.7889 (tppt) REVERT: B 104 ASN cc_start: 0.8172 (m-40) cc_final: 0.7815 (m110) REVERT: B 189 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8746 (mt) REVERT: C 34 GLN cc_start: 0.8556 (tp40) cc_final: 0.7957 (tm-30) REVERT: D 38 LEU cc_start: 0.7201 (mt) cc_final: 0.6737 (tp) REVERT: E 543 TYR cc_start: 0.5728 (m-80) cc_final: 0.5258 (m-80) outliers start: 37 outliers final: 32 residues processed: 191 average time/residue: 0.1466 time to fit residues: 42.2529 Evaluate side-chains 192 residues out of total 1717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 20 optimal weight: 0.0170 chunk 126 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 144 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 GLN A 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.158140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106276 restraints weight = 25346.472| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.40 r_work: 0.3175 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17630 Z= 0.116 Angle : 0.565 12.714 24290 Z= 0.268 Chirality : 0.043 0.328 2830 Planarity : 0.003 0.042 2811 Dihedral : 9.744 174.691 3046 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.07 % Allowed : 17.00 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 1953 helix: 1.26 (0.18), residues: 886 sheet: -0.21 (0.37), residues: 190 loop : -0.80 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 579 TYR 0.021 0.001 TYR E 31 PHE 0.014 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (17609) covalent geometry : angle 0.55815 / 0.27 (24274) hydrogen bonds : bond 0.03211 / 2.15 ( 840) hydrogen bonds : angle 4.03838 / 2.82 ( 2277) metal coordination : bond 0.00549 / 0.33 ( 20) metal coordination : angle 3.39900 / 1.86 ( 16) Misc. bond : bond 0.00043 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5185.24 seconds wall clock time: 89 minutes 28.25 seconds (5368.25 seconds total)