Starting phenix.real_space_refine on Thu Mar 5 10:39:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b5l_12037/03_2026/7b5l_12037.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5l_12037/03_2026/7b5l_12037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b5l_12037/03_2026/7b5l_12037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5l_12037/03_2026/7b5l_12037.map" model { file = "/net/cci-nas-00/data/ceres_data/7b5l_12037/03_2026/7b5l_12037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5l_12037/03_2026/7b5l_12037.cif" } resolution = 3.8 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= 0.004 sd= 0.862 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: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 2 5.49 5 S 130 5.16 5 C 13728 2.51 5 N 3684 2.21 5 O 3976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21529 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5752 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 693} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3472 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 410} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "T" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2536 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 598 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain: "S" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1097 Classifications: {'peptide': 138} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "R" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 677 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1209 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 137} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2279 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'TPO:plan-1': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "Y" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2046 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 239} Chain breaks: 2 Chain: "P" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 654 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' ZN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "U" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'SY8': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7609 SG CYS H 344 91.472 50.148 33.201 1.00142.28 S ATOM 7631 SG CYS H 347 89.245 50.637 36.488 1.00142.89 S ATOM 7742 SG CYS H 362 91.405 47.667 36.004 1.00148.38 S ATOM 7781 SG CYS H 367 88.429 47.997 34.022 1.00154.73 S ATOM 7821 SG CYS H 372 101.917 50.024 25.828 1.00178.27 S ATOM 7848 SG CYS H 375 99.520 51.922 23.723 1.00190.17 S ATOM 7942 SG CYS H 389 103.116 53.175 23.665 1.00219.08 S ATOM 7064 SG CYS H 276 76.255 60.293 51.404 1.00 78.74 S ATOM 7097 SG CYS H 281 74.600 58.093 53.713 1.00 99.03 S ATOM 7228 SG CYS H 297 72.585 59.950 51.252 1.00 97.07 S ATOM 7243 SG CYS H 299 74.357 61.771 54.339 1.00104.29 S ATOM 7284 SG CYS H 304 77.058 67.589 39.648 1.00 69.40 S ATOM 7309 SG CYS H 307 80.925 67.033 40.481 1.00 70.84 S ATOM 7391 SG CYS H 317 79.847 68.261 37.142 1.00 53.07 S ATOM 6338 SG CYS H 186 89.213 16.520 44.695 1.00164.95 S ATOM 6361 SG CYS H 189 90.281 15.607 48.121 1.00167.07 S ATOM 6519 SG CYS H 208 87.012 16.990 47.633 1.00151.78 S ATOM 6542 SG CYS H 211 89.903 19.338 47.462 1.00137.55 S ATOM 6479 SG CYS H 203 81.888 22.552 34.268 1.00157.38 S ATOM 6700 SG CYS H 231 84.276 23.751 36.843 1.00109.67 S ATOM 6732 SG CYS H 236 84.728 24.760 32.994 1.00123.72 S ATOM 14836 SG CYS R 42 70.829 99.319 30.991 1.00 41.28 S ATOM 14855 SG CYS R 45 70.958 97.691 34.628 1.00 47.24 S ATOM 15103 SG CYS R 83 72.694 100.890 33.918 1.00 51.39 S ATOM 15032 SG CYS R 75 74.625 101.065 18.259 1.00 72.61 S ATOM 15199 SG CYS R 94 76.290 99.591 21.488 1.00 63.53 S ATOM 14922 SG CYS R 53 71.061 103.261 37.805 1.00 59.15 S ATOM 14945 SG CYS R 56 69.613 106.349 39.425 1.00 64.60 S ATOM 14982 SG CYS R 68 68.265 104.935 36.002 1.00 64.01 S Time building chain proxies: 4.70, per 1000 atoms: 0.22 Number of scatterers: 21529 At special positions: 0 Unit cell: (178.76, 185.3, 160.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 130 16.00 P 2 15.00 O 3976 8.00 N 3684 7.00 C 13728 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 additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY U 75 " - pdb=" N SY8 U 101 " Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 935.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 347 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 344 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 367 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 362 " pdb=" ZN H 602 " pdb="ZN ZN H 602 " - pdb=" NE2 HIS H 382 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 372 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 375 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 389 " pdb=" ZN H 603 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 297 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 276 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 299 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 281 " pdb=" ZN H 604 " pdb="ZN ZN H 604 " - pdb=" NE2 HIS H 312 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 307 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 304 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 317 " pdb=" ZN H 605 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 208 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 189 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 211 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 186 " pdb=" ZN H 606 " pdb="ZN ZN H 606 " - pdb=" ND1 HIS H 205 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 231 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 203 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 236 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " Number of angles added : 33 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5098 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 24 sheets defined 54.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'C' and resid 18 through 32 removed outlier: 4.159A pdb=" N ASP C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 53 removed outlier: 3.526A pdb=" N TYR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 106 removed outlier: 3.838A pdb=" N ASP C 106 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 137 removed outlier: 4.179A pdb=" N GLN C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.575A pdb=" N HIS C 143 " --> pdb=" O TYR C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 172 Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.874A pdb=" N GLY C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 253 removed outlier: 3.712A pdb=" N THR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 275 removed outlier: 3.786A pdb=" N TYR C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 299 through 313 Processing helix chain 'C' and resid 317 through 329 removed outlier: 3.832A pdb=" N ILE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 354 removed outlier: 4.348A pdb=" N LEU C 336 " --> pdb=" O GLY C 332 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS C 338 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.563A pdb=" N ALA C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 361 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 removed outlier: 3.790A pdb=" N SER C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 405 Processing helix chain 'C' and resid 406 through 412 Processing helix chain 'C' and resid 417 through 431 Processing helix chain 'C' and resid 438 through 456 removed outlier: 3.602A pdb=" N VAL C 451 " --> pdb=" O ASN C 447 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 476 Processing helix chain 'C' and resid 481 through 497 Processing helix chain 'C' and resid 501 through 525 removed outlier: 3.559A pdb=" N GLN C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE C 511 " --> pdb=" O MET C 507 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 520 " --> pdb=" O ASP C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 528 No H-bonds generated for 'chain 'C' and resid 526 through 528' Processing helix chain 'C' and resid 559 through 574 removed outlier: 3.564A pdb=" N ARG C 573 " --> pdb=" O PHE C 569 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS C 574 " --> pdb=" O TYR C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 586 removed outlier: 3.539A pdb=" N SER C 586 " --> pdb=" O TYR C 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 586' Processing helix chain 'C' and resid 604 through 614 removed outlier: 3.736A pdb=" N TYR C 614 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 630 Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 706 through 722 Processing helix chain 'C' and resid 727 through 739 Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'H' and resid 105 through 125 removed outlier: 3.749A pdb=" N MET H 113 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL H 114 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL H 123 " --> pdb=" O GLU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 138 Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 154 through 160 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 209 through 223 Processing helix chain 'H' and resid 241 through 249 removed outlier: 3.824A pdb=" N VAL H 245 " --> pdb=" O ASP H 241 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 249 " --> pdb=" O VAL H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 270 Processing helix chain 'H' and resid 316 through 326 removed outlier: 4.171A pdb=" N LYS H 326 " --> pdb=" O LYS H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 341 removed outlier: 3.546A pdb=" N TRP H 336 " --> pdb=" O GLU H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 430 Processing helix chain 'H' and resid 430 through 448 removed outlier: 3.584A pdb=" N HIS H 448 " --> pdb=" O GLU H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 481 removed outlier: 4.400A pdb=" N TYR H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 477 " --> pdb=" O MET H 473 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR H 481 " --> pdb=" O VAL H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 513 removed outlier: 4.355A pdb=" N PHE H 491 " --> pdb=" O GLN H 487 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA H 496 " --> pdb=" O GLU H 492 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP H 497 " --> pdb=" O ASN H 493 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU H 510 " --> pdb=" O SER H 506 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG H 511 " --> pdb=" O GLY H 507 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 550 removed outlier: 3.946A pdb=" N GLN H 523 " --> pdb=" O GLN H 519 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR H 531 " --> pdb=" O ASP H 527 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 100 Processing helix chain 'T' and resid 101 through 110 Processing helix chain 'T' and resid 113 through 121 removed outlier: 3.612A pdb=" N SER T 121 " --> pdb=" O LEU T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 131 Processing helix chain 'T' and resid 148 through 158 Processing helix chain 'T' and resid 194 through 203 Processing helix chain 'T' and resid 219 through 227 Processing helix chain 'T' and resid 244 through 255 Processing helix chain 'T' and resid 270 through 281 Processing helix chain 'T' and resid 298 through 309 Processing helix chain 'T' and resid 324 through 334 removed outlier: 3.767A pdb=" N LEU T 334 " --> pdb=" O GLU T 330 " (cutoff:3.500A) Processing helix chain 'T' and resid 351 through 357 removed outlier: 4.192A pdb=" N GLU T 355 " --> pdb=" O GLU T 351 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU T 356 " --> pdb=" O THR T 352 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY T 357 " --> pdb=" O LEU T 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 351 through 357' Processing helix chain 'T' and resid 374 through 383 removed outlier: 3.721A pdb=" N LEU T 378 " --> pdb=" O GLY T 374 " (cutoff:3.500A) Processing helix chain 'T' and resid 408 through 412 removed outlier: 4.063A pdb=" N GLY T 411 " --> pdb=" O GLU T 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 30 Processing helix chain 'K' and resid 39 through 47 Processing helix chain 'S' and resid 18 through 22 Processing helix chain 'S' and resid 24 through 32 Processing helix chain 'S' and resid 45 through 59 removed outlier: 3.644A pdb=" N LYS S 51 " --> pdb=" O ALA S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 93 Processing helix chain 'S' and resid 96 through 111 removed outlier: 3.550A pdb=" N LEU S 100 " --> pdb=" O ASP S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 128 Processing helix chain 'S' and resid 131 through 140 Processing helix chain 'S' and resid 149 through 156 Processing helix chain 'U' and resid 22 through 34 Processing helix chain 'U' and resid 55 through 60 Processing helix chain 'N' and resid 22 through 35 removed outlier: 4.120A pdb=" N LYS N 33 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 3.578A pdb=" N ARG R 86 " --> pdb=" O HIS R 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 18 removed outlier: 3.524A pdb=" N LYS D 9 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 114 removed outlier: 3.698A pdb=" N VAL D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 132 through 146 removed outlier: 4.069A pdb=" N PHE D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LYS D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 87 through 94 Processing helix chain 'L' and resid 100 through 121 Processing helix chain 'L' and resid 145 through 149 removed outlier: 4.435A pdb=" N LEU L 148 " --> pdb=" O ASP L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 169 removed outlier: 3.614A pdb=" N ARG L 169 " --> pdb=" O LEU L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 175 Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.767A pdb=" N TRP L 187 " --> pdb=" O ALA L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 207 through 220 Processing helix chain 'L' and resid 247 through 252 removed outlier: 3.569A pdb=" N VAL L 252 " --> pdb=" O PHE L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 265 Processing helix chain 'L' and resid 276 through 282 removed outlier: 3.821A pdb=" N ALA L 282 " --> pdb=" O LYS L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 283 through 288 Processing helix chain 'Y' and resid 178 through 193 removed outlier: 4.412A pdb=" N VAL Y 191 " --> pdb=" O ARG Y 187 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS Y 192 " --> pdb=" O GLU Y 188 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS Y 193 " --> pdb=" O MET Y 189 " (cutoff:3.500A) Processing helix chain 'Y' and resid 198 through 203 removed outlier: 4.115A pdb=" N LYS Y 202 " --> pdb=" O GLY Y 198 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN Y 203 " --> pdb=" O TYR Y 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 198 through 203' Processing helix chain 'Y' and resid 207 through 225 Processing helix chain 'Y' and resid 228 through 244 removed outlier: 3.523A pdb=" N LEU Y 232 " --> pdb=" O GLN Y 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 249 through 251 No H-bonds generated for 'chain 'Y' and resid 249 through 251' Processing helix chain 'Y' and resid 252 through 269 Processing helix chain 'Y' and resid 274 through 282 removed outlier: 3.548A pdb=" N PHE Y 278 " --> pdb=" O GLU Y 274 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR Y 282 " --> pdb=" O PHE Y 278 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 303 Processing helix chain 'Y' and resid 310 through 320 removed outlier: 3.839A pdb=" N PHE Y 314 " --> pdb=" O THR Y 310 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU Y 320 " --> pdb=" O THR Y 316 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 343 removed outlier: 3.949A pdb=" N ASP Y 343 " --> pdb=" O LEU Y 339 " (cutoff:3.500A) Processing helix chain 'Y' and resid 346 through 350 Processing helix chain 'Y' and resid 351 through 369 Processing helix chain 'Y' and resid 373 through 381 removed outlier: 3.789A pdb=" N ILE Y 377 " --> pdb=" O PRO Y 373 " (cutoff:3.500A) Processing helix chain 'Y' and resid 383 through 401 Proline residue: Y 389 - end of helix Processing helix chain 'Y' and resid 402 through 404 No H-bonds generated for 'chain 'Y' and resid 402 through 404' Processing helix chain 'Y' and resid 407 through 413 Processing helix chain 'Y' and resid 414 through 419 removed outlier: 6.459A pdb=" N LYS Y 417 " --> pdb=" O LYS Y 414 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 424 removed outlier: 3.760A pdb=" N LEU Y 423 " --> pdb=" O GLY Y 420 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU Y 424 " --> pdb=" O VAL Y 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 420 through 424' Processing helix chain 'P' and resid 38 through 50 Processing helix chain 'P' and resid 53 through 61 removed outlier: 3.782A pdb=" N GLN P 57 " --> pdb=" O GLU P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 90 Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 540 removed outlier: 6.084A pdb=" N ASP C 534 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA R 29 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 534 through 540 removed outlier: 6.084A pdb=" N ASP C 534 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA R 29 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TRP R 33 " --> pdb=" O GLN C 538 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 540 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS R 26 " --> pdb=" O GLU C 589 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 601 through 602 Processing sheet with id=AA4, first strand: chain 'C' and resid 619 through 621 removed outlier: 4.169A pdb=" N TYR C 620 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 725 through 726 Processing sheet with id=AA6, first strand: chain 'H' and resid 101 through 104 Processing sheet with id=AA7, first strand: chain 'H' and resid 198 through 199 Processing sheet with id=AA8, first strand: chain 'H' and resid 294 through 296 Processing sheet with id=AA9, first strand: chain 'H' and resid 342 through 343 Processing sheet with id=AB1, first strand: chain 'H' and resid 359 through 361 Processing sheet with id=AB2, first strand: chain 'T' and resid 162 through 164 Processing sheet with id=AB3, first strand: chain 'T' and resid 260 through 262 removed outlier: 3.720A pdb=" N ASP T 316 " --> pdb=" O LEU T 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 7 through 8 removed outlier: 3.663A pdb=" N TYR K 12 " --> pdb=" O TYR K 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 7 through 8 removed outlier: 9.062A pdb=" N ILE K 66 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE K 59 " --> pdb=" O ILE K 66 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU K 68 " --> pdb=" O TYR K 57 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 14 through 17 Processing sheet with id=AB7, first strand: chain 'U' and resid 10 through 16 removed outlier: 5.529A pdb=" N LYS U 11 " --> pdb=" O THR U 7 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR U 7 " --> pdb=" O LYS U 11 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU U 69 " --> pdb=" O LYS U 6 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE U 45 " --> pdb=" O LYS U 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 2 through 6 Processing sheet with id=AB9, first strand: chain 'N' and resid 48 through 49 Processing sheet with id=AC1, first strand: chain 'R' and resid 78 through 80 removed outlier: 4.046A pdb=" N LYS R 105 " --> pdb=" O TRP R 72 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 22 through 27 removed outlier: 4.569A pdb=" N ASN D 24 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D 38 " --> pdb=" O ASN D 24 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 31 through 36 removed outlier: 4.030A pdb=" N ASP L 68 " --> pdb=" O VAL L 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 85 through 86 removed outlier: 3.585A pdb=" N GLN L 85 " --> pdb=" O ILE L 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 123 through 124 removed outlier: 3.647A pdb=" N ARG L 150 " --> pdb=" O LEU L 124 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 62 through 63 1014 hydrogen bonds defined for protein. 2940 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6995 1.34 - 1.47: 4999 1.47 - 1.59: 9782 1.59 - 1.71: 6 1.71 - 1.84: 186 Bond restraints: 21968 Sorted by residual: bond pdb=" OG1 TPO L 160 " pdb=" P TPO L 160 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" OG1 TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.717 1.614 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" O1P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.525 1.609 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" O2P TPO P 187 " pdb=" P TPO P 187 " ideal model delta sigma weight residual 1.528 1.611 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" O2P TPO L 160 " pdb=" P TPO L 160 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.66e+01 ... (remaining 21963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 29142 2.44 - 4.87: 483 4.87 - 7.31: 54 7.31 - 9.75: 11 9.75 - 12.19: 5 Bond angle restraints: 29695 Sorted by residual: angle pdb=" N PRO S 2 " pdb=" CA PRO S 2 " pdb=" CB PRO S 2 " ideal model delta sigma weight residual 103.00 109.80 -6.80 1.10e+00 8.26e-01 3.83e+01 angle pdb=" C ALA C 218 " pdb=" N PHE C 219 " pdb=" CA PHE C 219 " ideal model delta sigma weight residual 121.54 132.04 -10.50 1.91e+00 2.74e-01 3.02e+01 angle pdb=" N ASP P 51 " pdb=" CA ASP P 51 " pdb=" C ASP P 51 " ideal model delta sigma weight residual 114.04 108.31 5.73 1.24e+00 6.50e-01 2.13e+01 angle pdb=" C ARG C 745 " pdb=" N VAL C 746 " pdb=" CA VAL C 746 " ideal model delta sigma weight residual 120.24 123.11 -2.87 6.30e-01 2.52e+00 2.08e+01 angle pdb=" CA ARG H 511 " pdb=" CB ARG H 511 " pdb=" CG ARG H 511 " ideal model delta sigma weight residual 114.10 122.72 -8.62 2.00e+00 2.50e-01 1.86e+01 ... (remaining 29690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 11899 17.76 - 35.52: 1183 35.52 - 53.28: 200 53.28 - 71.04: 52 71.04 - 88.80: 12 Dihedral angle restraints: 13346 sinusoidal: 5515 harmonic: 7831 Sorted by residual: dihedral pdb=" CA ILE H 513 " pdb=" C ILE H 513 " pdb=" N SER H 514 " pdb=" CA SER H 514 " ideal model delta harmonic sigma weight residual 180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA VAL L 163 " pdb=" C VAL L 163 " pdb=" N VAL L 164 " pdb=" CA VAL L 164 " ideal model delta harmonic sigma weight residual 180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" C VAL L 163 " pdb=" N VAL L 163 " pdb=" CA VAL L 163 " pdb=" CB VAL L 163 " ideal model delta harmonic sigma weight residual -122.00 -134.86 12.86 0 2.50e+00 1.60e-01 2.65e+01 ... (remaining 13343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3015 0.079 - 0.157: 279 0.157 - 0.236: 7 0.236 - 0.314: 0 0.314 - 0.393: 1 Chirality restraints: 3302 Sorted by residual: chirality pdb=" CA VAL L 163 " pdb=" N VAL L 163 " pdb=" C VAL L 163 " pdb=" CB VAL L 163 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA ILE H 513 " pdb=" N ILE H 513 " pdb=" C ILE H 513 " pdb=" CB ILE H 513 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU T 356 " pdb=" CB LEU T 356 " pdb=" CD1 LEU T 356 " pdb=" CD2 LEU T 356 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 3299 not shown) Planarity restraints: 3782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 237 " 0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO L 238 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO L 238 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 238 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 291 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.23e+00 pdb=" N PRO L 292 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO L 292 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 292 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 509 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C LEU H 509 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU H 509 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU H 510 " 0.013 2.00e-02 2.50e+03 ... (remaining 3779 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 295 2.57 - 3.16: 19300 3.16 - 3.74: 33254 3.74 - 4.32: 44298 4.32 - 4.90: 71817 Nonbonded interactions: 168964 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.993 2.230 nonbonded pdb=" NH1 ARG C 168 " pdb=" OD1 ASP C 169 " model vdw 2.138 3.120 nonbonded pdb=" OG SER C 234 " pdb=" OE1 GLN C 235 " model vdw 2.154 3.040 nonbonded pdb=" O ILE H 337 " pdb=" OG1 THR H 341 " model vdw 2.196 3.040 nonbonded pdb=" O LEU C 735 " pdb=" OG SER C 739 " model vdw 2.204 3.040 ... (remaining 168959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.040 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.006 0.272 22007 Z= 0.293 Angle : 0.797 12.186 29730 Z= 0.431 Chirality : 0.045 0.393 3302 Planarity : 0.005 0.080 3781 Dihedral : 14.534 88.797 8247 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 0.04 % Allowed : 0.72 % Favored : 99.24 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.16), residues: 2598 helix: 0.27 (0.14), residues: 1282 sheet: -1.96 (0.41), residues: 149 loop : -2.63 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 473 TYR 0.029 0.002 TYR H 529 PHE 0.021 0.002 PHE D 70 TRP 0.019 0.002 TRP K 43 HIS 0.008 0.001 HIS H 312 Details of bonding type rmsd covalent geometry : bond 0.00592 (21968) covalent geometry : angle 0.77542 (29695) hydrogen bonds : bond 0.13709 ( 1012) hydrogen bonds : angle 6.47651 ( 2940) metal coordination : bond 0.05070 ( 35) metal coordination : angle 5.50118 ( 33) Misc. bond : bond 0.08616 ( 3) link_TRANS : bond 0.01848 ( 1) link_TRANS : angle 3.84572 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7101 (ppp) cc_final: 0.6856 (ppp) REVERT: C 599 TYR cc_start: 0.8146 (m-80) cc_final: 0.7739 (m-10) REVERT: K 26 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8341 (tmtt) REVERT: K 49 GLN cc_start: 0.8347 (mp10) cc_final: 0.7984 (mp-120) REVERT: N 25 ARG cc_start: 0.9492 (tpt-90) cc_final: 0.8565 (mmm160) REVERT: N 28 GLU cc_start: 0.9368 (tm-30) cc_final: 0.8444 (tm-30) REVERT: N 51 ASN cc_start: 0.8760 (t0) cc_final: 0.8284 (t0) REVERT: D 8 MET cc_start: 0.9129 (tmm) cc_final: 0.8885 (tmm) REVERT: D 75 TYR cc_start: 0.8587 (t80) cc_final: 0.8163 (t80) REVERT: D 143 PHE cc_start: 0.9334 (t80) cc_final: 0.9035 (t80) REVERT: D 147 TYR cc_start: 0.8907 (m-80) cc_final: 0.8264 (m-80) REVERT: L 71 HIS cc_start: 0.8885 (t70) cc_final: 0.8348 (t-90) REVERT: L 167 TRP cc_start: 0.9386 (m-10) cc_final: 0.8851 (m100) REVERT: Y 242 PHE cc_start: 0.9469 (t80) cc_final: 0.9242 (t80) REVERT: P 52 MET cc_start: 0.7287 (ttt) cc_final: 0.6003 (ppp) REVERT: P 74 TYR cc_start: 0.8991 (m-10) cc_final: 0.8262 (m-80) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.1632 time to fit residues: 59.0288 Evaluate side-chains 180 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 258 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 224 ASN ** T 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 325 ASN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 41 GLN N 41 GLN R 76 ASN D 84 GLN L 113 GLN Y 361 HIS Y 404 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.089713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.063017 restraints weight = 96967.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064382 restraints weight = 63808.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.064361 restraints weight = 45125.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.064768 restraints weight = 41112.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064790 restraints weight = 40177.590| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 22007 Z= 0.251 Angle : 0.712 10.534 29730 Z= 0.366 Chirality : 0.044 0.175 3302 Planarity : 0.005 0.073 3781 Dihedral : 5.264 34.989 2868 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.93 % Allowed : 8.63 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.17), residues: 2598 helix: 0.65 (0.14), residues: 1300 sheet: -1.92 (0.39), residues: 165 loop : -2.41 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 473 TYR 0.031 0.002 TYR H 529 PHE 0.031 0.002 PHE H 457 TRP 0.022 0.002 TRP K 43 HIS 0.009 0.001 HIS Y 179 Details of bonding type rmsd covalent geometry : bond 0.00579 (21968) covalent geometry : angle 0.70124 (29695) hydrogen bonds : bond 0.06178 ( 1012) hydrogen bonds : angle 5.40252 ( 2940) metal coordination : bond 0.01359 ( 35) metal coordination : angle 3.71020 ( 33) Misc. bond : bond 0.00644 ( 3) link_TRANS : bond 0.00145 ( 1) link_TRANS : angle 0.10681 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 608 MET cc_start: 0.8985 (mtt) cc_final: 0.8711 (mtt) REVERT: K 26 LYS cc_start: 0.8598 (mtmm) cc_final: 0.8279 (tmtt) REVERT: S 146 THR cc_start: 0.6067 (OUTLIER) cc_final: 0.5853 (m) REVERT: N 17 ILE cc_start: 0.9666 (pt) cc_final: 0.9415 (mp) REVERT: N 25 ARG cc_start: 0.9399 (tpt-90) cc_final: 0.8877 (mmm160) REVERT: N 28 GLU cc_start: 0.9362 (tm-30) cc_final: 0.8802 (tm-30) REVERT: N 51 ASN cc_start: 0.9124 (t0) cc_final: 0.8745 (t0) REVERT: D 8 MET cc_start: 0.9118 (tmm) cc_final: 0.8806 (tmm) REVERT: D 43 ASN cc_start: 0.9082 (t0) cc_final: 0.8834 (t0) REVERT: D 75 TYR cc_start: 0.8796 (t80) cc_final: 0.8332 (t80) REVERT: D 80 ASP cc_start: 0.8290 (t70) cc_final: 0.8083 (t70) REVERT: D 147 TYR cc_start: 0.9065 (m-80) cc_final: 0.8387 (m-80) REVERT: L 136 ASN cc_start: 0.8703 (p0) cc_final: 0.8374 (p0) REVERT: Y 179 HIS cc_start: 0.8446 (m-70) cc_final: 0.8119 (m-70) REVERT: Y 294 MET cc_start: 0.9230 (ttm) cc_final: 0.8872 (mmp) REVERT: P 52 MET cc_start: 0.7856 (ttt) cc_final: 0.6701 (ppp) REVERT: P 59 LYS cc_start: 0.9305 (pttm) cc_final: 0.8999 (pttm) REVERT: P 74 TYR cc_start: 0.8975 (m-10) cc_final: 0.8319 (m-80) REVERT: P 77 GLN cc_start: 0.8662 (mp10) cc_final: 0.8412 (mp10) REVERT: P 81 LYS cc_start: 0.7157 (mmtt) cc_final: 0.6363 (mmtt) REVERT: P 89 TYR cc_start: 0.9318 (p90) cc_final: 0.8979 (p90) outliers start: 22 outliers final: 13 residues processed: 227 average time/residue: 0.1552 time to fit residues: 54.6630 Evaluate side-chains 204 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain Y residue 208 ASN Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 390 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 81 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 187 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 HIS ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 231 ASN ** T 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.092018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067277 restraints weight = 98483.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.067789 restraints weight = 61042.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068196 restraints weight = 44124.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068328 restraints weight = 45545.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068337 restraints weight = 37778.934| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22007 Z= 0.122 Angle : 0.602 12.317 29730 Z= 0.308 Chirality : 0.041 0.219 3302 Planarity : 0.004 0.070 3781 Dihedral : 4.776 33.524 2868 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.26 % Allowed : 11.49 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.60 (0.17), residues: 2598 helix: 1.15 (0.15), residues: 1305 sheet: -1.84 (0.38), residues: 174 loop : -2.11 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 154 TYR 0.025 0.001 TYR H 529 PHE 0.023 0.001 PHE H 457 TRP 0.020 0.001 TRP K 43 HIS 0.007 0.001 HIS Y 179 Details of bonding type rmsd covalent geometry : bond 0.00260 (21968) covalent geometry : angle 0.59478 (29695) hydrogen bonds : bond 0.04627 ( 1012) hydrogen bonds : angle 4.78955 ( 2940) metal coordination : bond 0.00493 ( 35) metal coordination : angle 2.78082 ( 33) Misc. bond : bond 0.00054 ( 3) link_TRANS : bond 0.00067 ( 1) link_TRANS : angle 0.02214 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 585 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9478 (pp) REVERT: T 322 MET cc_start: 0.7859 (mtt) cc_final: 0.7084 (ppp) REVERT: K 26 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8207 (tmtt) REVERT: S 146 THR cc_start: 0.6290 (OUTLIER) cc_final: 0.6070 (m) REVERT: U 18 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8545 (mp0) REVERT: N 5 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8809 (m) REVERT: N 25 ARG cc_start: 0.9367 (tpt-90) cc_final: 0.8744 (mmm160) REVERT: N 28 GLU cc_start: 0.9314 (tm-30) cc_final: 0.8010 (tm-30) REVERT: N 29 ARG cc_start: 0.9287 (tpp80) cc_final: 0.8904 (tpp80) REVERT: N 45 TYR cc_start: 0.8278 (t80) cc_final: 0.7996 (t80) REVERT: N 51 ASN cc_start: 0.9106 (t0) cc_final: 0.8247 (t0) REVERT: N 53 GLU cc_start: 0.9658 (pp20) cc_final: 0.9383 (pp20) REVERT: N 54 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8306 (mtmm) REVERT: D 43 ASN cc_start: 0.9079 (t0) cc_final: 0.8785 (t0) REVERT: D 75 TYR cc_start: 0.8790 (t80) cc_final: 0.8328 (t80) REVERT: D 80 ASP cc_start: 0.8253 (t70) cc_final: 0.8028 (t70) REVERT: D 147 TYR cc_start: 0.9194 (m-80) cc_final: 0.8457 (m-80) REVERT: L 158 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8811 (p) REVERT: L 265 GLN cc_start: 0.8449 (pm20) cc_final: 0.8195 (pm20) REVERT: Y 179 HIS cc_start: 0.8451 (m-70) cc_final: 0.8247 (m-70) REVERT: Y 189 MET cc_start: 0.9385 (mmm) cc_final: 0.9182 (mmm) REVERT: Y 294 MET cc_start: 0.9338 (ttm) cc_final: 0.9043 (ttp) REVERT: P 52 MET cc_start: 0.7892 (ttt) cc_final: 0.6883 (ppp) REVERT: P 59 LYS cc_start: 0.9282 (pttm) cc_final: 0.9018 (pttm) REVERT: P 74 TYR cc_start: 0.8912 (m-10) cc_final: 0.8191 (m-80) REVERT: P 77 GLN cc_start: 0.8710 (mp10) cc_final: 0.8455 (mp10) REVERT: P 81 LYS cc_start: 0.7110 (mmtt) cc_final: 0.6789 (mmtt) outliers start: 30 outliers final: 15 residues processed: 241 average time/residue: 0.1538 time to fit residues: 57.3802 Evaluate side-chains 215 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain Y residue 208 ASN Chi-restraints excluded: chain Y residue 283 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 229 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 201 optimal weight: 0.0020 chunk 218 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 345 HIS ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.091457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.066745 restraints weight = 97940.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067197 restraints weight = 60188.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066906 restraints weight = 45811.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067269 restraints weight = 48373.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.067376 restraints weight = 41289.186| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22007 Z= 0.140 Angle : 0.598 10.288 29730 Z= 0.304 Chirality : 0.041 0.192 3302 Planarity : 0.004 0.073 3781 Dihedral : 4.650 33.482 2868 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.64 % Allowed : 13.13 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.43 (0.17), residues: 2598 helix: 1.30 (0.15), residues: 1310 sheet: -1.73 (0.39), residues: 174 loop : -2.06 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 23 TYR 0.026 0.001 TYR H 529 PHE 0.025 0.001 PHE H 457 TRP 0.021 0.001 TRP K 43 HIS 0.005 0.001 HIS Y 179 Details of bonding type rmsd covalent geometry : bond 0.00317 (21968) covalent geometry : angle 0.59020 (29695) hydrogen bonds : bond 0.04655 ( 1012) hydrogen bonds : angle 4.71135 ( 2940) metal coordination : bond 0.00679 ( 35) metal coordination : angle 2.89521 ( 33) Misc. bond : bond 0.00012 ( 3) link_TRANS : bond 0.00092 ( 1) link_TRANS : angle 0.05447 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 585 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9356 (pp) REVERT: H 508 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.6910 (t80) REVERT: K 26 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8224 (tmtt) REVERT: S 146 THR cc_start: 0.6270 (OUTLIER) cc_final: 0.6028 (m) REVERT: U 18 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8555 (mp0) REVERT: N 25 ARG cc_start: 0.9321 (tpt-90) cc_final: 0.8794 (mmm160) REVERT: N 28 GLU cc_start: 0.9274 (tm-30) cc_final: 0.8714 (tm-30) REVERT: N 51 ASN cc_start: 0.9136 (t0) cc_final: 0.8256 (t0) REVERT: N 53 GLU cc_start: 0.9626 (pp20) cc_final: 0.9357 (pp20) REVERT: N 54 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8287 (mtmm) REVERT: D 75 TYR cc_start: 0.8799 (t80) cc_final: 0.8336 (t80) REVERT: D 80 ASP cc_start: 0.8254 (t70) cc_final: 0.8035 (t70) REVERT: D 147 TYR cc_start: 0.9185 (m-80) cc_final: 0.8639 (m-80) REVERT: L 71 HIS cc_start: 0.8860 (t70) cc_final: 0.8383 (t70) REVERT: L 164 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7839 (p) REVERT: Y 294 MET cc_start: 0.9306 (ttm) cc_final: 0.8894 (mmp) REVERT: Y 378 ARG cc_start: 0.9381 (ttp-110) cc_final: 0.8986 (ptp90) REVERT: P 52 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.6942 (ppp) REVERT: P 59 LYS cc_start: 0.9281 (pttm) cc_final: 0.9021 (pttm) REVERT: P 73 LYS cc_start: 0.9289 (tppt) cc_final: 0.8908 (tppt) REVERT: P 74 TYR cc_start: 0.8942 (m-10) cc_final: 0.8137 (m-80) REVERT: P 77 GLN cc_start: 0.8844 (mp10) cc_final: 0.8630 (mp10) outliers start: 39 outliers final: 20 residues processed: 234 average time/residue: 0.1496 time to fit residues: 54.6261 Evaluate side-chains 216 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 390 CYS Chi-restraints excluded: chain P residue 52 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 154 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 115 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 245 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 437 GLN ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.091965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.067277 restraints weight = 97390.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067780 restraints weight = 59869.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.067663 restraints weight = 44075.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067990 restraints weight = 48490.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.068204 restraints weight = 39772.987| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22007 Z= 0.122 Angle : 0.582 14.464 29730 Z= 0.296 Chirality : 0.040 0.171 3302 Planarity : 0.004 0.074 3781 Dihedral : 4.510 32.944 2868 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.98 % Allowed : 13.97 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.26 (0.17), residues: 2598 helix: 1.39 (0.15), residues: 1311 sheet: -1.49 (0.38), residues: 186 loop : -1.94 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 90 TYR 0.024 0.001 TYR H 529 PHE 0.026 0.001 PHE H 457 TRP 0.020 0.001 TRP K 43 HIS 0.005 0.001 HIS P 48 Details of bonding type rmsd covalent geometry : bond 0.00270 (21968) covalent geometry : angle 0.57496 (29695) hydrogen bonds : bond 0.04333 ( 1012) hydrogen bonds : angle 4.56364 ( 2940) metal coordination : bond 0.00458 ( 35) metal coordination : angle 2.74731 ( 33) Misc. bond : bond 0.00022 ( 3) link_TRANS : bond 0.00074 ( 1) link_TRANS : angle 0.04075 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.6883 (ppp) cc_final: 0.6591 (ppp) REVERT: C 585 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9288 (pp) REVERT: H 508 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7203 (t80) REVERT: T 322 MET cc_start: 0.7757 (mtt) cc_final: 0.6958 (ppp) REVERT: K 26 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8143 (tmtt) REVERT: S 146 THR cc_start: 0.6525 (OUTLIER) cc_final: 0.6319 (m) REVERT: U 18 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8532 (mp0) REVERT: N 25 ARG cc_start: 0.9325 (tpt-90) cc_final: 0.8918 (mmm160) REVERT: N 28 GLU cc_start: 0.9305 (tm-30) cc_final: 0.8713 (tm-30) REVERT: N 51 ASN cc_start: 0.9108 (t0) cc_final: 0.8320 (t0) REVERT: N 53 GLU cc_start: 0.9642 (pp20) cc_final: 0.9442 (pp20) REVERT: N 54 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8429 (mtmm) REVERT: D 75 TYR cc_start: 0.8739 (t80) cc_final: 0.8397 (t80) REVERT: D 80 ASP cc_start: 0.8259 (t70) cc_final: 0.8032 (t70) REVERT: D 147 TYR cc_start: 0.9181 (m-80) cc_final: 0.8658 (m-80) REVERT: L 71 HIS cc_start: 0.8874 (t70) cc_final: 0.8348 (t-90) REVERT: L 164 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7746 (p) REVERT: Y 294 MET cc_start: 0.9326 (ttm) cc_final: 0.8896 (mmp) REVERT: Y 378 ARG cc_start: 0.9402 (ttp-110) cc_final: 0.9031 (ptp90) REVERT: P 52 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.6872 (ppp) REVERT: P 77 GLN cc_start: 0.8789 (mp10) cc_final: 0.8554 (mp10) outliers start: 47 outliers final: 17 residues processed: 242 average time/residue: 0.1499 time to fit residues: 56.2066 Evaluate side-chains 209 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain P residue 52 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 245 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 47 optimal weight: 0.0000 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.090766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.065659 restraints weight = 97118.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066149 restraints weight = 59436.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065793 restraints weight = 44344.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066185 restraints weight = 48491.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.066252 restraints weight = 41012.289| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22007 Z= 0.182 Angle : 0.628 10.830 29730 Z= 0.319 Chirality : 0.042 0.173 3302 Planarity : 0.004 0.075 3781 Dihedral : 4.585 34.392 2868 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.06 % Allowed : 14.60 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.27 (0.17), residues: 2598 helix: 1.33 (0.15), residues: 1316 sheet: -1.46 (0.39), residues: 187 loop : -1.90 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 23 TYR 0.028 0.001 TYR H 529 PHE 0.028 0.001 PHE H 457 TRP 0.023 0.001 TRP K 43 HIS 0.008 0.001 HIS Y 179 Details of bonding type rmsd covalent geometry : bond 0.00419 (21968) covalent geometry : angle 0.61854 (29695) hydrogen bonds : bond 0.04951 ( 1012) hydrogen bonds : angle 4.69261 ( 2940) metal coordination : bond 0.00979 ( 35) metal coordination : angle 3.26123 ( 33) Misc. bond : bond 0.00020 ( 3) link_TRANS : bond 0.00119 ( 1) link_TRANS : angle 0.07211 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 585 LEU cc_start: 0.9681 (OUTLIER) cc_final: 0.9264 (pp) REVERT: H 508 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7142 (t80) REVERT: T 224 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8655 (m110) REVERT: T 322 MET cc_start: 0.7858 (mtt) cc_final: 0.6942 (ppp) REVERT: K 49 GLN cc_start: 0.8644 (mp10) cc_final: 0.8367 (mp10) REVERT: S 146 THR cc_start: 0.6485 (OUTLIER) cc_final: 0.6273 (m) REVERT: U 18 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8481 (mp0) REVERT: N 25 ARG cc_start: 0.9493 (tpt-90) cc_final: 0.9008 (mmm160) REVERT: N 28 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8773 (tm-30) REVERT: N 51 ASN cc_start: 0.9145 (t0) cc_final: 0.8339 (t0) REVERT: N 53 GLU cc_start: 0.9640 (pp20) cc_final: 0.9439 (pp20) REVERT: N 54 LYS cc_start: 0.8786 (mtpt) cc_final: 0.8424 (mtmm) REVERT: D 75 TYR cc_start: 0.8719 (t80) cc_final: 0.8411 (t80) REVERT: D 147 TYR cc_start: 0.9161 (m-80) cc_final: 0.8641 (m-80) REVERT: L 38 ASP cc_start: 0.5544 (OUTLIER) cc_final: 0.4834 (p0) REVERT: L 91 MET cc_start: 0.8180 (mtm) cc_final: 0.7827 (ptp) REVERT: Y 294 MET cc_start: 0.9334 (ttm) cc_final: 0.8913 (ttm) REVERT: Y 378 ARG cc_start: 0.9366 (ttp-110) cc_final: 0.8902 (mtm110) REVERT: P 52 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7008 (ppp) REVERT: P 77 GLN cc_start: 0.8838 (mp10) cc_final: 0.8594 (mp10) outliers start: 49 outliers final: 31 residues processed: 234 average time/residue: 0.1494 time to fit residues: 54.7565 Evaluate side-chains 220 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain T residue 224 ASN Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 196 MET Chi-restraints excluded: chain L residue 255 LEU Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 409 ILE Chi-restraints excluded: chain P residue 52 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 143 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 206 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 597 ASN ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 395 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.090075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.063988 restraints weight = 97085.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.065184 restraints weight = 60053.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065686 restraints weight = 40596.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065795 restraints weight = 43411.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.065735 restraints weight = 36199.558| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22007 Z= 0.232 Angle : 0.669 10.887 29730 Z= 0.340 Chirality : 0.043 0.185 3302 Planarity : 0.004 0.078 3781 Dihedral : 4.724 36.712 2868 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.19 % Allowed : 15.40 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.48 (0.17), residues: 2598 helix: 1.12 (0.15), residues: 1334 sheet: -1.60 (0.39), residues: 178 loop : -1.97 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 561 TYR 0.029 0.002 TYR H 529 PHE 0.029 0.002 PHE H 457 TRP 0.025 0.001 TRP K 43 HIS 0.008 0.001 HIS Y 179 Details of bonding type rmsd covalent geometry : bond 0.00537 (21968) covalent geometry : angle 0.65800 (29695) hydrogen bonds : bond 0.05352 ( 1012) hydrogen bonds : angle 4.79856 ( 2940) metal coordination : bond 0.01289 ( 35) metal coordination : angle 3.65811 ( 33) Misc. bond : bond 0.00016 ( 3) link_TRANS : bond 0.00151 ( 1) link_TRANS : angle 0.08083 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7121 (ppp) cc_final: 0.6737 (ppp) REVERT: C 585 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9298 (pp) REVERT: H 508 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7064 (t80) REVERT: T 224 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8665 (m110) REVERT: T 322 MET cc_start: 0.7686 (mtt) cc_final: 0.7214 (ppp) REVERT: K 49 GLN cc_start: 0.8605 (mp10) cc_final: 0.8239 (pm20) REVERT: U 18 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8485 (mp0) REVERT: N 25 ARG cc_start: 0.9497 (tpt-90) cc_final: 0.8975 (mmm160) REVERT: N 28 GLU cc_start: 0.9315 (tm-30) cc_final: 0.8813 (tm-30) REVERT: N 51 ASN cc_start: 0.9069 (t0) cc_final: 0.8300 (t0) REVERT: N 54 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8443 (mtmm) REVERT: D 75 TYR cc_start: 0.8684 (t80) cc_final: 0.8359 (t80) REVERT: L 38 ASP cc_start: 0.5454 (OUTLIER) cc_final: 0.4756 (p0) REVERT: L 71 HIS cc_start: 0.8905 (t70) cc_final: 0.8112 (t-90) REVERT: L 91 MET cc_start: 0.8124 (mtm) cc_final: 0.7881 (ptp) REVERT: Y 200 MET cc_start: 0.8701 (tpp) cc_final: 0.8376 (tpp) REVERT: Y 294 MET cc_start: 0.9360 (ttm) cc_final: 0.8933 (ttm) REVERT: Y 378 ARG cc_start: 0.9345 (ttp-110) cc_final: 0.8894 (mtm110) REVERT: P 52 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.6861 (ppp) REVERT: P 77 GLN cc_start: 0.8805 (mp10) cc_final: 0.8553 (mp10) outliers start: 52 outliers final: 35 residues processed: 227 average time/residue: 0.1539 time to fit residues: 55.0158 Evaluate side-chains 220 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain T residue 224 ASN Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 196 MET Chi-restraints excluded: chain L residue 255 LEU Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain Y residue 181 ASP Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain P residue 52 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.090519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.065262 restraints weight = 97093.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065872 restraints weight = 59900.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.065484 restraints weight = 45269.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.065883 restraints weight = 47789.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.066004 restraints weight = 40862.433| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22007 Z= 0.181 Angle : 0.646 11.187 29730 Z= 0.327 Chirality : 0.042 0.169 3302 Planarity : 0.004 0.077 3781 Dihedral : 4.672 36.606 2868 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.98 % Allowed : 16.33 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.40 (0.17), residues: 2598 helix: 1.19 (0.15), residues: 1333 sheet: -1.61 (0.39), residues: 179 loop : -1.94 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 154 TYR 0.026 0.001 TYR H 529 PHE 0.028 0.001 PHE H 457 TRP 0.023 0.001 TRP K 43 HIS 0.008 0.001 HIS Y 179 Details of bonding type rmsd covalent geometry : bond 0.00417 (21968) covalent geometry : angle 0.63677 (29695) hydrogen bonds : bond 0.05015 ( 1012) hydrogen bonds : angle 4.69743 ( 2940) metal coordination : bond 0.00935 ( 35) metal coordination : angle 3.40581 ( 33) Misc. bond : bond 0.00013 ( 3) link_TRANS : bond 0.00122 ( 1) link_TRANS : angle 0.06232 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.7006 (ppp) cc_final: 0.6667 (ppp) REVERT: C 585 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9326 (pp) REVERT: H 197 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8594 (m-80) REVERT: H 508 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7206 (t80) REVERT: T 224 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8664 (m110) REVERT: T 322 MET cc_start: 0.7608 (mtt) cc_final: 0.7095 (ppp) REVERT: U 18 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8495 (mp0) REVERT: N 25 ARG cc_start: 0.9472 (tpt-90) cc_final: 0.9024 (mmm160) REVERT: N 28 GLU cc_start: 0.9295 (tm-30) cc_final: 0.8922 (tm-30) REVERT: D 75 TYR cc_start: 0.8623 (t80) cc_final: 0.8309 (t80) REVERT: D 147 TYR cc_start: 0.8943 (m-80) cc_final: 0.8235 (m-10) REVERT: L 38 ASP cc_start: 0.5502 (OUTLIER) cc_final: 0.4788 (p0) REVERT: L 71 HIS cc_start: 0.8892 (t70) cc_final: 0.8121 (t-90) REVERT: Y 200 MET cc_start: 0.8711 (tpp) cc_final: 0.8410 (tpp) REVERT: Y 294 MET cc_start: 0.9331 (ttm) cc_final: 0.8894 (ttm) REVERT: P 52 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.6970 (ppp) REVERT: P 77 GLN cc_start: 0.8836 (mp10) cc_final: 0.8575 (mp10) outliers start: 47 outliers final: 33 residues processed: 223 average time/residue: 0.1475 time to fit residues: 52.2266 Evaluate side-chains 219 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain T residue 224 ASN Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 333 GLN Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 196 MET Chi-restraints excluded: chain L residue 255 LEU Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 311 VAL Chi-restraints excluded: chain P residue 52 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 91 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 204 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 67 optimal weight: 0.0060 chunk 134 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 overall best weight: 1.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.090792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066135 restraints weight = 96852.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066733 restraints weight = 56329.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066248 restraints weight = 45460.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066583 restraints weight = 49026.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066679 restraints weight = 41793.339| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22007 Z= 0.166 Angle : 0.651 12.224 29730 Z= 0.327 Chirality : 0.042 0.320 3302 Planarity : 0.004 0.077 3781 Dihedral : 4.608 36.298 2868 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.06 % Allowed : 16.12 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.35 (0.17), residues: 2598 helix: 1.23 (0.15), residues: 1332 sheet: -1.63 (0.39), residues: 181 loop : -1.90 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG S 154 TYR 0.026 0.001 TYR H 529 PHE 0.027 0.001 PHE H 457 TRP 0.023 0.001 TRP Y 217 HIS 0.007 0.001 HIS Y 179 Details of bonding type rmsd covalent geometry : bond 0.00383 (21968) covalent geometry : angle 0.64262 (29695) hydrogen bonds : bond 0.04854 ( 1012) hydrogen bonds : angle 4.66223 ( 2940) metal coordination : bond 0.00832 ( 35) metal coordination : angle 3.27201 ( 33) Misc. bond : bond 0.00015 ( 3) link_TRANS : bond 0.00113 ( 1) link_TRANS : angle 0.05529 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.6985 (ppp) cc_final: 0.6658 (ppp) REVERT: C 585 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9331 (pp) REVERT: H 197 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8608 (m-80) REVERT: H 508 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7203 (t80) REVERT: T 224 ASN cc_start: 0.9085 (OUTLIER) cc_final: 0.8657 (m110) REVERT: T 322 MET cc_start: 0.7672 (mtt) cc_final: 0.7078 (ppp) REVERT: U 18 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8455 (mp0) REVERT: N 25 ARG cc_start: 0.9502 (tpt-90) cc_final: 0.9056 (mmm160) REVERT: N 28 GLU cc_start: 0.9321 (tm-30) cc_final: 0.8895 (tm-30) REVERT: N 29 ARG cc_start: 0.9670 (mmm160) cc_final: 0.9302 (mmm-85) REVERT: D 75 TYR cc_start: 0.8629 (t80) cc_final: 0.8327 (t80) REVERT: D 147 TYR cc_start: 0.8992 (m-80) cc_final: 0.8317 (m-10) REVERT: L 38 ASP cc_start: 0.5420 (OUTLIER) cc_final: 0.4703 (p0) REVERT: L 248 PHE cc_start: 0.7521 (t80) cc_final: 0.7093 (t80) REVERT: Y 200 MET cc_start: 0.8753 (tpp) cc_final: 0.8476 (tpp) REVERT: Y 294 MET cc_start: 0.9332 (ttm) cc_final: 0.8899 (ttm) REVERT: P 52 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.6966 (ppp) REVERT: P 68 LYS cc_start: 0.9520 (mmmt) cc_final: 0.9106 (mmmt) REVERT: P 77 GLN cc_start: 0.8780 (mp10) cc_final: 0.8527 (mp10) outliers start: 49 outliers final: 38 residues processed: 223 average time/residue: 0.1481 time to fit residues: 52.1089 Evaluate side-chains 221 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain T residue 224 ASN Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 333 GLN Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 255 LEU Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 283 ASP Chi-restraints excluded: chain Y residue 311 VAL Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain P residue 59 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 214 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 252 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 117 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 359 HIS ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 395 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.091929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067286 restraints weight = 97715.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067894 restraints weight = 59773.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.067685 restraints weight = 43036.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068044 restraints weight = 49077.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.068104 restraints weight = 39602.306| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22007 Z= 0.120 Angle : 0.641 12.438 29730 Z= 0.320 Chirality : 0.041 0.244 3302 Planarity : 0.004 0.076 3781 Dihedral : 4.505 33.514 2868 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.85 % Allowed : 16.75 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.18 (0.17), residues: 2598 helix: 1.37 (0.15), residues: 1331 sheet: -1.45 (0.41), residues: 171 loop : -1.84 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 154 TYR 0.022 0.001 TYR H 529 PHE 0.024 0.001 PHE Y 319 TRP 0.025 0.001 TRP Y 217 HIS 0.007 0.001 HIS Y 179 Details of bonding type rmsd covalent geometry : bond 0.00265 (21968) covalent geometry : angle 0.63455 (29695) hydrogen bonds : bond 0.04252 ( 1012) hydrogen bonds : angle 4.50065 ( 2940) metal coordination : bond 0.00381 ( 35) metal coordination : angle 2.78120 ( 33) Misc. bond : bond 0.00021 ( 3) link_TRANS : bond 0.00071 ( 1) link_TRANS : angle 0.03326 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5196 Ramachandran restraints generated. 2598 Oldfield, 0 Emsley, 2598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.6946 (ppp) cc_final: 0.6634 (ppp) REVERT: H 197 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: H 508 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7433 (t80) REVERT: T 224 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8620 (m110) REVERT: T 322 MET cc_start: 0.7690 (mtt) cc_final: 0.6836 (ppp) REVERT: N 25 ARG cc_start: 0.9468 (tpt-90) cc_final: 0.9014 (mmm160) REVERT: N 28 GLU cc_start: 0.9303 (tm-30) cc_final: 0.8911 (tm-30) REVERT: N 59 TYR cc_start: 0.8569 (m-80) cc_final: 0.8238 (m-80) REVERT: D 75 TYR cc_start: 0.8604 (t80) cc_final: 0.8298 (t80) REVERT: D 147 TYR cc_start: 0.8987 (m-80) cc_final: 0.8293 (m-10) REVERT: L 38 ASP cc_start: 0.5445 (OUTLIER) cc_final: 0.4719 (p0) REVERT: L 71 HIS cc_start: 0.8851 (t70) cc_final: 0.8071 (t-90) REVERT: L 164 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7670 (p) REVERT: L 167 TRP cc_start: 0.9299 (m-10) cc_final: 0.8909 (m100) REVERT: L 248 PHE cc_start: 0.7440 (t80) cc_final: 0.7006 (t80) REVERT: Y 200 MET cc_start: 0.8737 (tpp) cc_final: 0.8453 (tpp) REVERT: Y 294 MET cc_start: 0.9315 (ttm) cc_final: 0.8882 (ttm) REVERT: P 52 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7069 (ppp) REVERT: P 68 LYS cc_start: 0.9571 (mmmt) cc_final: 0.9134 (mmmt) REVERT: P 77 GLN cc_start: 0.8820 (mp10) cc_final: 0.8561 (mp10) REVERT: P 89 TYR cc_start: 0.9156 (p90) cc_final: 0.8851 (p90) outliers start: 44 outliers final: 31 residues processed: 227 average time/residue: 0.1413 time to fit residues: 51.5160 Evaluate side-chains 225 residues out of total 2407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain H residue 162 HIS Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain T residue 224 ASN Chi-restraints excluded: chain T residue 284 THR Chi-restraints excluded: chain T residue 333 GLN Chi-restraints excluded: chain T residue 349 ILE Chi-restraints excluded: chain T residue 409 ILE Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 118 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 255 LEU Chi-restraints excluded: chain L residue 268 HIS Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain P residue 59 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 12 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 182 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.091938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067076 restraints weight = 97643.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067809 restraints weight = 61718.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.067722 restraints weight = 42238.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068006 restraints weight = 45435.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068004 restraints weight = 40482.238| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 22007 Z= 0.128 Angle : 0.651 11.887 29730 Z= 0.324 Chirality : 0.041 0.223 3302 Planarity : 0.004 0.073 3781 Dihedral : 4.442 32.868 2868 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.73 % Allowed : 16.88 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.14 (0.17), residues: 2598 helix: 1.38 (0.15), residues: 1334 sheet: -1.39 (0.41), residues: 170 loop : -1.80 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 23 TYR 0.023 0.001 TYR H 529 PHE 0.022 0.001 PHE H 457 TRP 0.026 0.001 TRP Y 217 HIS 0.005 0.001 HIS P 48 Details of bonding type rmsd covalent geometry : bond 0.00292 (21968) covalent geometry : angle 0.64470 (29695) hydrogen bonds : bond 0.04230 ( 1012) hydrogen bonds : angle 4.46508 ( 2940) metal coordination : bond 0.00449 ( 35) metal coordination : angle 2.74264 ( 33) Misc. bond : bond 0.00024 ( 3) link_TRANS : bond 0.00074 ( 1) link_TRANS : angle 0.03405 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3864.37 seconds wall clock time: 67 minutes 32.47 seconds (4052.47 seconds total)