Starting phenix.real_space_refine on Tue Feb 20 14:00:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqy_13034/02_2024/7oqy_13034_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqy_13034/02_2024/7oqy_13034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqy_13034/02_2024/7oqy_13034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqy_13034/02_2024/7oqy_13034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqy_13034/02_2024/7oqy_13034_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqy_13034/02_2024/7oqy_13034_updated.pdb" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 3 7.16 5 Zn 8 6.06 5 Mg 1 5.21 5 S 140 5.16 5 C 17800 2.51 5 N 4836 2.21 5 O 5244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B GLU 759": "OE1" <-> "OE2" Residue "B GLU 1116": "OE1" <-> "OE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "G GLU 15": "OE1" <-> "OE2" Residue "G GLU 36": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "H GLU 74": "OE1" <-> "OE2" Residue "K GLU 8": "OE1" <-> "OE2" Residue "L GLU 86": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28032 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 6984 Classifications: {'peptide': 875} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 822} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 8718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8718 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1051} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3024 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2039 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1421 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 175} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 856 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 987 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 608 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 690 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 707 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "N" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 534 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "P" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 376 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 43} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "Y" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'F3S': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 427 SG CYS A 58 51.440 75.409 58.203 1.00 99.56 S ATOM 447 SG CYS A 61 51.843 71.624 57.653 1.00 96.69 S ATOM 489 SG CYS A 68 54.084 73.455 60.135 1.00 87.51 S ATOM 736 SG CYS A 98 86.427 81.994 23.952 1.00122.96 S ATOM 767 SG CYS A 101 84.630 79.035 22.262 1.00124.29 S ATOM 1154 SG CYS A 146 88.475 79.210 22.330 1.00134.49 S ATOM 1177 SG CYS A 149 86.290 81.435 20.140 1.00136.57 S ATOM 4560 SG CYS A 575 118.163 37.912 103.565 1.00 79.02 S ATOM 4600 SG CYS A 580 114.810 37.995 103.990 1.00 67.50 S ATOM 15221 SG CYS B1060 59.135 62.746 46.290 1.00 83.18 S ATOM 15244 SG CYS B1063 61.494 65.402 46.204 1.00 81.50 S ATOM 15375 SG CYS B1078 58.252 65.740 47.958 1.00 97.82 S ATOM 20141 SG CYS D 183 101.510 55.703 136.503 1.00 33.83 S ATOM 20316 SG CYS D 206 100.947 54.351 132.141 1.00 30.60 S ATOM 20340 SG CYS D 209 104.453 51.316 134.631 1.00 39.33 S ATOM 20294 SG CYS D 203 98.374 50.855 135.816 1.00 26.41 S ATOM 26090 SG CYS N 7 82.059 68.606 125.881 1.00 15.43 S ATOM 26114 SG CYS N 10 81.465 65.520 128.196 1.00 19.36 S ATOM 26377 SG CYS N 44 85.060 66.590 127.087 1.00 18.89 S ATOM 26383 SG CYS N 45 83.083 68.407 129.631 1.00 19.95 S ATOM 26611 SG CYS P 6 59.193 104.635 111.898 1.00 68.49 S ATOM 26761 SG CYS P 26 56.892 106.336 112.093 1.00 77.41 S ATOM 26786 SG CYS P 29 59.542 107.834 112.775 1.00 81.37 S ATOM 27331 SG CYS Y 4 135.606 123.465 61.403 1.00114.11 S ATOM 27449 SG CYS Y 20 134.033 121.216 58.368 1.00128.01 S ATOM 27776 SG CYS Y 63 119.614 63.090 80.396 1.00 48.53 S ATOM 27800 SG CYS Y 66 118.898 66.777 79.665 1.00 50.77 S ATOM 27940 SG CYS Y 83 120.617 65.833 82.843 1.00 45.55 S ATOM 27961 SG CYS Y 86 116.949 64.987 82.402 1.00 48.87 S Time building chain proxies: 15.13, per 1000 atoms: 0.54 Number of scatterers: 28032 At special positions: 0 Unit cell: (160.58, 151.9, 162.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 Fe 3 26.01 S 140 16.00 Mg 1 11.99 O 5244 8.00 N 4836 7.00 C 17800 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.91 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S D 301 " pdb="FE4 F3S D 301 " - pdb=" SG CYS D 203 " pdb="FE3 F3S D 301 " - pdb=" SG CYS D 209 " pdb="FE1 F3S D 301 " - pdb=" SG CYS D 183 " pdb="FE1 F3S D 301 " - pdb=" SG CYS D 206 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 71 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 68 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 61 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 58 " pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 149 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 101 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 146 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 98 " pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 580 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 575 " pdb="ZN ZN A 904 " - pdb=" ND1 HIS A 582 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" NE2 HIS B1081 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1060 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1063 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1078 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 45 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 10 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 7 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 29 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 6 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 26 " pdb=" ZN Y 101 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 20 " pdb="ZN ZN Y 101 " - pdb=" SG CYS Y 4 " pdb=" ZN Y 102 " pdb="ZN ZN Y 102 " - pdb=" SG CYS Y 66 " pdb="ZN ZN Y 102 " - pdb=" SG CYS Y 83 " pdb="ZN ZN Y 102 " - pdb=" SG CYS Y 86 " pdb="ZN ZN Y 102 " - pdb=" SG CYS Y 63 " Number of angles added : 24 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6590 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 32 sheets defined 33.5% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.693A pdb=" N VAL A 87 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LYS A 88 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR A 91 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 95 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.854A pdb=" N ARG A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.900A pdb=" N ARG A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 234 through 254 removed outlier: 4.065A pdb=" N ASP A 241 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 277 removed outlier: 4.135A pdb=" N LEU A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.633A pdb=" N CYS A 450 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Proline residue: A 451 - end of helix No H-bonds generated for 'chain 'A' and resid 447 through 453' Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 518 through 527 removed outlier: 4.306A pdb=" N VAL A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 555 removed outlier: 3.745A pdb=" N LEU A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 570 removed outlier: 3.637A pdb=" N LYS A 570 " --> pdb=" O ASN A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 570' Processing helix chain 'A' and resid 600 through 603 No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 611 through 619 Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 631 through 642 removed outlier: 3.613A pdb=" N PHE A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 636 " --> pdb=" O PHE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 651 removed outlier: 3.824A pdb=" N ILE A 651 " --> pdb=" O LEU A 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 648 through 651' Processing helix chain 'A' and resid 655 through 680 Processing helix chain 'A' and resid 695 through 717 Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 803 through 807 removed outlier: 3.764A pdb=" N VAL A 807 " --> pdb=" O GLU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 868 through 876 Processing helix chain 'B' and resid 4 through 17 Processing helix chain 'B' and resid 22 through 43 removed outlier: 3.751A pdb=" N SER B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 221 through 228 removed outlier: 3.738A pdb=" N LEU B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 244 through 257 removed outlier: 4.015A pdb=" N GLU B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Proline residue: B 252 - end of helix removed outlier: 3.661A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.806A pdb=" N ARG B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 291 Processing helix chain 'B' and resid 297 through 299 No H-bonds generated for 'chain 'B' and resid 297 through 299' Processing helix chain 'B' and resid 303 through 324 removed outlier: 3.761A pdb=" N ARG B 306 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS B 307 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS B 308 " --> pdb=" O ASP B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 344 through 368 removed outlier: 3.523A pdb=" N ALA B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 382 No H-bonds generated for 'chain 'B' and resid 379 through 382' Processing helix chain 'B' and resid 388 through 398 Processing helix chain 'B' and resid 417 through 425 removed outlier: 3.709A pdb=" N ARG B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 509 through 514 removed outlier: 3.944A pdb=" N SER B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 543 Processing helix chain 'B' and resid 589 through 596 Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 618 through 621 Processing helix chain 'B' and resid 628 through 630 No H-bonds generated for 'chain 'B' and resid 628 through 630' Processing helix chain 'B' and resid 642 through 645 removed outlier: 4.005A pdb=" N ILE B 645 " --> pdb=" O PRO B 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 642 through 645' Processing helix chain 'B' and resid 650 through 652 No H-bonds generated for 'chain 'B' and resid 650 through 652' Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 661 through 672 removed outlier: 3.576A pdb=" N SER B 668 " --> pdb=" O ASN B 664 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 669 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS B 672 " --> pdb=" O SER B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 684 No H-bonds generated for 'chain 'B' and resid 682 through 684' Processing helix chain 'B' and resid 704 through 708 removed outlier: 3.957A pdb=" N VAL B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 708' Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 765 through 767 No H-bonds generated for 'chain 'B' and resid 765 through 767' Processing helix chain 'B' and resid 784 through 786 No H-bonds generated for 'chain 'B' and resid 784 through 786' Processing helix chain 'B' and resid 910 through 912 No H-bonds generated for 'chain 'B' and resid 910 through 912' Processing helix chain 'B' and resid 919 through 934 Processing helix chain 'B' and resid 949 through 958 Processing helix chain 'B' and resid 996 through 998 No H-bonds generated for 'chain 'B' and resid 996 through 998' Processing helix chain 'B' and resid 1029 through 1038 Processing helix chain 'B' and resid 1041 through 1048 Processing helix chain 'B' and resid 1094 through 1105 Processing helix chain 'C' and resid 4 through 14 Processing helix chain 'C' and resid 23 through 35 removed outlier: 3.714A pdb=" N ASP C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 60 removed outlier: 3.594A pdb=" N SER C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 179 through 187 Processing helix chain 'C' and resid 215 through 225 Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.574A pdb=" N ASN C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 282 Processing helix chain 'C' and resid 284 through 302 removed outlier: 4.005A pdb=" N GLN C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 339 through 345 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'D' and resid 22 through 34 removed outlier: 3.917A pdb=" N ILE D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 63 Processing helix chain 'D' and resid 72 through 75 No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 79 through 81 No H-bonds generated for 'chain 'D' and resid 79 through 81' Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 154 through 156 No H-bonds generated for 'chain 'D' and resid 154 through 156' Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 238 through 263 removed outlier: 3.592A pdb=" N LEU D 242 " --> pdb=" O PRO D 238 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 243 " --> pdb=" O GLU D 239 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 34 Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 171 through 181 Processing helix chain 'F' and resid 15 through 29 removed outlier: 4.697A pdb=" N THR F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 45 removed outlier: 4.176A pdb=" N SER F 44 " --> pdb=" O ASP F 40 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE F 45 " --> pdb=" O TYR F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 59 Processing helix chain 'F' and resid 67 through 76 removed outlier: 3.621A pdb=" N VAL F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 87 No H-bonds generated for 'chain 'F' and resid 84 through 87' Processing helix chain 'F' and resid 98 through 108 removed outlier: 3.638A pdb=" N GLU F 106 " --> pdb=" O GLN F 102 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 35 Processing helix chain 'H' and resid 39 through 41 No H-bonds generated for 'chain 'H' and resid 39 through 41' Processing helix chain 'H' and resid 50 through 55 removed outlier: 3.545A pdb=" N SER H 54 " --> pdb=" O PRO H 50 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE H 55 " --> pdb=" O VAL H 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 50 through 55' Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 20 through 34 Processing helix chain 'K' and resid 52 through 61 Processing helix chain 'L' and resid 22 through 34 removed outlier: 3.777A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 89 removed outlier: 3.555A pdb=" N LYS L 88 " --> pdb=" O ILE L 84 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS L 89 " --> pdb=" O ASP L 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 26 removed outlier: 3.578A pdb=" N TRP N 18 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU N 19 " --> pdb=" O ASP N 16 " (cutoff:3.500A) Proline residue: N 20 - end of helix removed outlier: 3.541A pdb=" N VAL N 25 " --> pdb=" O SER N 22 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET N 26 " --> pdb=" O ASN N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 38 Processing helix chain 'N' and resid 43 through 50 removed outlier: 3.704A pdb=" N MET N 48 " --> pdb=" O CYS N 44 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU N 49 " --> pdb=" O CYS N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 4.675A pdb=" N HIS N 61 " --> pdb=" O ARG N 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 57 Processing helix chain 'Q' and resid 63 through 76 Processing sheet with id= A, first strand: chain 'A' and resid 73 through 76 Processing sheet with id= B, first strand: chain 'A' and resid 156 through 159 Processing sheet with id= C, first strand: chain 'A' and resid 321 through 325 Processing sheet with id= D, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.072A pdb=" N PHE A 443 " --> pdb=" O SER A 327 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.752A pdb=" N TYR A 377 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N HIS A 410 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA A 375 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 562 through 565 Processing sheet with id= G, first strand: chain 'A' and resid 830 through 832 Processing sheet with id= H, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.885A pdb=" N GLY B 115 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 96 " --> pdb=" O TYR B 113 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TYR B 113 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N MET B 98 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU B 111 " --> pdb=" O MET B 98 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 60 through 62 Processing sheet with id= J, first strand: chain 'B' and resid 150 through 152 Processing sheet with id= K, first strand: chain 'B' and resid 339 through 342 removed outlier: 3.548A pdb=" N ALA B 161 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 171 through 174 removed outlier: 6.675A pdb=" N ARG B 202 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 184 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 200 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS B 186 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 198 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 188 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL B 196 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 552 through 557 removed outlier: 6.295A pdb=" N LYS B 517 " --> pdb=" O VAL B 564 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE B 566 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR B 519 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 520 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 575 through 578 Processing sheet with id= O, first strand: chain 'B' and resid 689 through 693 removed outlier: 6.050A pdb=" N ARG B 865 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL B 845 " --> pdb=" O ARG B 865 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 906 through 908 removed outlier: 4.440A pdb=" N LEU B 983 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N MET B 738 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU B 889 " --> pdb=" O MET B 738 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 1054 through 1060 Processing sheet with id= R, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.510A pdb=" N MET C 120 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 151 through 157 removed outlier: 6.882A pdb=" N GLN C 166 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL C 154 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR C 164 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL C 156 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER C 162 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 204 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER C 203 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP C 200 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR C 205 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP C 198 " --> pdb=" O THR C 205 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 3 through 9 removed outlier: 6.910A pdb=" N ARG D 14 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG D 8 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ARG D 12 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR D 167 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N ASN D 224 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 11.258A pdb=" N ARG D 165 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N PHE D 226 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N ILE D 163 " --> pdb=" O PHE D 226 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 94 through 101 removed outlier: 3.779A pdb=" N GLU D 43 " --> pdb=" O ARG D 144 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG D 146 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL D 41 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY D 148 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N MET D 39 " --> pdb=" O GLY D 148 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 107 through 109 removed outlier: 3.535A pdb=" N VAL D 131 " --> pdb=" O ILE D 109 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 188 through 190 Processing sheet with id= X, first strand: chain 'E' and resid 6 through 13 removed outlier: 4.241A pdb=" N ASN E 50 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 104 through 108 removed outlier: 5.849A pdb=" N ASN E 100 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL E 89 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 147 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ALA E 160 " --> pdb=" O ILE E 147 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 5 through 10 removed outlier: 3.550A pdb=" N GLY G 7 " --> pdb=" O PHE G 54 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP G 114 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU G 88 " --> pdb=" O PHE G 75 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU G 77 " --> pdb=" O ILE G 86 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE G 86 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU G 94 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE G 95 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP G 28 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE G 11 " --> pdb=" O ASP G 28 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 19 through 22 Processing sheet with id= AB, first strand: chain 'K' and resid 68 through 72 Processing sheet with id= AC, first strand: chain 'L' and resid 2 through 8 removed outlier: 6.622A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU L 8 " --> pdb=" O TYR L 12 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR L 12 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'P' and resid 14 through 16 Processing sheet with id= AE, first strand: chain 'Y' and resid 12 through 14 removed outlier: 3.548A pdb=" N LYS Y 12 " --> pdb=" O VAL Y 19 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Y' and resid 58 through 60 removed outlier: 6.668A pdb=" N LEU Y 80 " --> pdb=" O LEU Y 74 " (cutoff:3.500A) 896 hydrogen bonds defined for protein. 2529 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: 9.42 Time building geometry restraints manager: 10.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.80: 28436 1.80 - 2.41: 56 2.41 - 3.03: 0 3.03 - 3.64: 0 3.64 - 4.25: 3 Bond restraints: 28495 Sorted by residual: bond pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 2.258 4.228 -1.970 2.00e-02 2.50e+03 9.70e+03 bond pdb=" S4 F3S D 301 " pdb="FE1 F3S D 301 " ideal model delta sigma weight residual 2.233 4.183 -1.950 2.00e-02 2.50e+03 9.51e+03 bond pdb=" S2 F3S D 301 " pdb="FE3 F3S D 301 " ideal model delta sigma weight residual 2.300 4.249 -1.949 2.00e-02 2.50e+03 9.49e+03 bond pdb=" S2 F3S D 301 " pdb="FE4 F3S D 301 " ideal model delta sigma weight residual 2.317 2.205 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" S3 F3S D 301 " pdb="FE1 F3S D 301 " ideal model delta sigma weight residual 2.296 2.194 0.102 2.00e-02 2.50e+03 2.62e+01 ... (remaining 28490 not shown) Histogram of bond angle deviations from ideal: 39.84 - 61.10: 6 61.10 - 82.35: 4 82.35 - 103.61: 390 103.61 - 124.87: 37734 124.87 - 146.12: 324 Bond angle restraints: 38458 Sorted by residual: angle pdb=" S1 F3S D 301 " pdb="FE4 F3S D 301 " pdb=" S3 F3S D 301 " ideal model delta sigma weight residual 114.75 39.84 74.91 3.00e+00 1.11e-01 6.23e+02 angle pdb=" S3 F3S D 301 " pdb="FE1 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 112.59 41.42 71.17 3.00e+00 1.11e-01 5.63e+02 angle pdb=" S1 F3S D 301 " pdb="FE3 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 112.54 146.12 -33.58 3.00e+00 1.11e-01 1.25e+02 angle pdb="FE1 F3S D 301 " pdb=" S4 F3S D 301 " pdb="FE3 F3S D 301 " ideal model delta sigma weight residual 74.86 45.08 29.78 3.00e+00 1.11e-01 9.86e+01 angle pdb=" S2 F3S D 301 " pdb="FE3 F3S D 301 " pdb=" S4 F3S D 301 " ideal model delta sigma weight residual 103.26 74.40 28.86 3.00e+00 1.11e-01 9.26e+01 ... (remaining 38453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 15841 17.57 - 35.14: 1455 35.14 - 52.70: 213 52.70 - 70.27: 54 70.27 - 87.84: 19 Dihedral angle restraints: 17582 sinusoidal: 7338 harmonic: 10244 Sorted by residual: dihedral pdb=" CA VAL B1080 " pdb=" C VAL B1080 " pdb=" N HIS B1081 " pdb=" CA HIS B1081 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PHE B 212 " pdb=" C PHE B 212 " pdb=" N ALA B 213 " pdb=" CA ALA B 213 " ideal model delta harmonic sigma weight residual 180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ILE C 206 " pdb=" C ILE C 206 " pdb=" N TYR C 207 " pdb=" CA TYR C 207 " ideal model delta harmonic sigma weight residual 180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 17579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.548: 4382 2.548 - 5.095: 0 5.095 - 7.643: 0 7.643 - 10.191: 0 10.191 - 12.738: 1 Chirality restraints: 4383 Sorted by residual: chirality pdb=" S2 F3S D 301 " pdb="FE1 F3S D 301 " pdb="FE3 F3S D 301 " pdb="FE4 F3S D 301 " both_signs ideal model delta sigma weight residual False 10.77 -1.97 12.74 2.00e-01 2.50e+01 4.06e+03 chirality pdb=" CB ILE Y 92 " pdb=" CA ILE Y 92 " pdb=" CG1 ILE Y 92 " pdb=" CG2 ILE Y 92 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE C 21 " pdb=" N ILE C 21 " pdb=" C ILE C 21 " pdb=" CB ILE C 21 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.49e-01 ... (remaining 4380 not shown) Planarity restraints: 4927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B1081 " 0.035 2.00e-02 2.50e+03 4.05e-02 2.46e+01 pdb=" CG HIS B1081 " -0.087 2.00e-02 2.50e+03 pdb=" ND1 HIS B1081 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS B1081 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 HIS B1081 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B1081 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 33 " -0.013 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" C ILE C 33 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE C 33 " -0.018 2.00e-02 2.50e+03 pdb=" N MET C 34 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 302 " -0.031 5.00e-02 4.00e+02 4.79e-02 3.66e+00 pdb=" N PRO B 303 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 303 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 303 " -0.027 5.00e-02 4.00e+02 ... (remaining 4924 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 81 2.45 - 3.07: 17140 3.07 - 3.68: 40008 3.68 - 4.29: 63908 4.29 - 4.90: 107557 Nonbonded interactions: 228694 Sorted by model distance: nonbonded pdb=" OD1 ASP A 458 " pdb=" OD1 ASP A 460 " model vdw 1.842 3.040 nonbonded pdb=" CG HIS B1081 " pdb="ZN ZN B1201 " model vdw 1.928 1.960 nonbonded pdb=" O ARG A 573 " pdb="ZN ZN A 904 " model vdw 2.002 2.230 nonbonded pdb=" OD1 ASP A 458 " pdb="MG MG A 901 " model vdw 2.018 2.170 nonbonded pdb=" OE2 GLU P 12 " pdb="ZN ZN P 101 " model vdw 2.021 2.230 ... (remaining 228689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.030 Extract box with map and model: 9.340 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 80.590 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 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:10.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.020 1.970 28495 Z= 1.280 Angle : 0.875 74.909 38458 Z= 0.364 Chirality : 0.198 12.738 4383 Planarity : 0.004 0.048 4927 Dihedral : 13.679 87.837 10992 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3497 helix: 0.54 (0.16), residues: 1198 sheet: -0.10 (0.21), residues: 592 loop : -0.74 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 8 HIS 0.048 0.001 HIS B1081 PHE 0.014 0.001 PHE A 419 TYR 0.015 0.001 TYR A 91 ARG 0.005 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 3.097 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.7931 (ptt) cc_final: 0.7651 (ptt) REVERT: A 131 ARG cc_start: 0.6916 (mtm180) cc_final: 0.6647 (mtt90) REVERT: A 200 LYS cc_start: 0.8380 (ptpp) cc_final: 0.8114 (pttm) REVERT: A 267 ASP cc_start: 0.7413 (m-30) cc_final: 0.6919 (t0) REVERT: A 363 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8449 (mm-40) REVERT: A 458 ASP cc_start: 0.6273 (p0) cc_final: 0.5958 (p0) REVERT: A 646 MET cc_start: 0.8689 (ttt) cc_final: 0.8452 (ttt) REVERT: B 346 ASP cc_start: 0.7337 (m-30) cc_final: 0.7023 (m-30) REVERT: B 770 LYS cc_start: 0.8240 (mttp) cc_final: 0.8036 (mttm) REVERT: B 891 ASP cc_start: 0.7135 (m-30) cc_final: 0.6829 (m-30) REVERT: B 995 MET cc_start: 0.9012 (mtm) cc_final: 0.8783 (mtt) REVERT: C 34 MET cc_start: 0.8733 (mmt) cc_final: 0.8445 (mmt) REVERT: C 133 ASP cc_start: 0.6507 (m-30) cc_final: 0.6281 (m-30) REVERT: C 187 THR cc_start: 0.8125 (m) cc_final: 0.7871 (m) REVERT: C 246 GLU cc_start: 0.7869 (tt0) cc_final: 0.7585 (tt0) REVERT: D 18 GLU cc_start: 0.7995 (tt0) cc_final: 0.7787 (tt0) REVERT: E 163 MET cc_start: -0.1294 (mmp) cc_final: -0.1841 (tpp) REVERT: G 10 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7650 (ttmm) REVERT: G 15 GLU cc_start: 0.7392 (mp0) cc_final: 0.7155 (mp0) REVERT: G 50 GLU cc_start: 0.8468 (pt0) cc_final: 0.8115 (pt0) REVERT: N 19 GLU cc_start: 0.6864 (mp0) cc_final: 0.6546 (mp0) REVERT: Q 45 MET cc_start: 0.7770 (ttp) cc_final: 0.7328 (ttp) REVERT: Q 49 ASP cc_start: 0.7156 (m-30) cc_final: 0.6564 (m-30) REVERT: Y 77 LYS cc_start: 0.6708 (ptmt) cc_final: 0.6505 (ttpt) outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 1.7111 time to fit residues: 921.9624 Evaluate side-chains 413 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 293 optimal weight: 2.9990 chunk 263 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 271 optimal weight: 30.0000 chunk 105 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 315 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 GLN B 197 GLN B 245 GLN B 400 ASN B 582 ASN ** B 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 326 GLN D 75 HIS D 94 ASN ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 28495 Z= 0.348 Angle : 0.865 69.136 38458 Z= 0.376 Chirality : 0.054 1.454 4383 Planarity : 0.005 0.048 4927 Dihedral : 4.854 64.946 3884 Min Nonbonded Distance : 1.460 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.65 % Allowed : 8.16 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3497 helix: 0.37 (0.15), residues: 1215 sheet: -0.18 (0.21), residues: 593 loop : -0.80 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 8 HIS 0.013 0.002 HIS A 426 PHE 0.016 0.002 PHE G 37 TYR 0.024 0.002 TYR A 850 ARG 0.007 0.000 ARG Y 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 437 time to evaluate : 3.451 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.8065 (ptt) cc_final: 0.7687 (ptt) REVERT: A 200 LYS cc_start: 0.8416 (ptpp) cc_final: 0.8174 (pttm) REVERT: A 267 ASP cc_start: 0.7333 (m-30) cc_final: 0.6885 (t0) REVERT: A 346 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8110 (ttp) REVERT: A 359 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: A 363 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8433 (mm-40) REVERT: B 197 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: B 594 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8033 (mttp) REVERT: B 599 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: B 617 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: B 891 ASP cc_start: 0.7144 (m-30) cc_final: 0.6837 (m-30) REVERT: B 995 MET cc_start: 0.9095 (mtm) cc_final: 0.8797 (mtt) REVERT: B 1104 MET cc_start: 0.7806 (mtm) cc_final: 0.7555 (mtp) REVERT: C 44 GLU cc_start: 0.6997 (tt0) cc_final: 0.6794 (mp0) REVERT: C 133 ASP cc_start: 0.6517 (m-30) cc_final: 0.6288 (m-30) REVERT: C 187 THR cc_start: 0.8143 (m) cc_final: 0.7889 (m) REVERT: D 71 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: E 56 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7395 (tp30) REVERT: E 163 MET cc_start: -0.0224 (mmp) cc_final: -0.0746 (tpp) REVERT: G 15 GLU cc_start: 0.6741 (mp0) cc_final: 0.6278 (mp0) REVERT: G 50 GLU cc_start: 0.8481 (pt0) cc_final: 0.8002 (pt0) REVERT: G 99 LEU cc_start: 0.7293 (mm) cc_final: 0.7061 (mm) REVERT: H 67 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7691 (mtm180) REVERT: L 21 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7100 (pp20) REVERT: N 19 GLU cc_start: 0.6940 (mp0) cc_final: 0.6600 (mp0) REVERT: P 12 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: P 16 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8114 (p0) REVERT: Q 45 MET cc_start: 0.7634 (ttp) cc_final: 0.7010 (ttp) REVERT: Q 49 ASP cc_start: 0.7193 (m-30) cc_final: 0.6623 (m-30) REVERT: Y 77 LYS cc_start: 0.6793 (ptmt) cc_final: 0.6576 (ttpt) outliers start: 51 outliers final: 22 residues processed: 460 average time/residue: 1.7133 time to fit residues: 894.6186 Evaluate side-chains 453 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 420 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 16 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 262 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 315 optimal weight: 3.9990 chunk 341 optimal weight: 7.9990 chunk 281 optimal weight: 20.0000 chunk 313 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 253 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN B 197 GLN B 245 GLN B 400 ASN B 582 ASN ** B 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 375 GLN D 75 HIS D 94 ASN G 6 GLN H 13 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 28495 Z= 0.223 Angle : 0.785 77.685 38458 Z= 0.336 Chirality : 0.047 0.624 4383 Planarity : 0.004 0.049 4927 Dihedral : 4.636 63.740 3884 Min Nonbonded Distance : 1.529 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.00 % Allowed : 10.00 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3497 helix: 0.51 (0.15), residues: 1215 sheet: -0.08 (0.21), residues: 589 loop : -0.74 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 8 HIS 0.015 0.001 HIS B1081 PHE 0.017 0.002 PHE B 359 TYR 0.017 0.001 TYR A 850 ARG 0.008 0.000 ARG Y 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 427 time to evaluate : 3.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.7979 (ptt) cc_final: 0.7521 (ptt) REVERT: A 200 LYS cc_start: 0.8415 (ptpp) cc_final: 0.8198 (pttm) REVERT: A 267 ASP cc_start: 0.7364 (m-30) cc_final: 0.6842 (t0) REVERT: A 346 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8060 (ttp) REVERT: A 359 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: A 363 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8457 (mm-40) REVERT: B 171 LEU cc_start: 0.8380 (mt) cc_final: 0.8156 (mt) REVERT: B 197 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: B 590 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6641 (mm-30) REVERT: B 594 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7928 (mttp) REVERT: B 599 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: B 617 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: B 835 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7567 (pt) REVERT: B 891 ASP cc_start: 0.7089 (m-30) cc_final: 0.6783 (m-30) REVERT: C 133 ASP cc_start: 0.6519 (m-30) cc_final: 0.6283 (m-30) REVERT: C 161 MET cc_start: 0.7062 (mmp) cc_final: 0.6079 (mmt) REVERT: C 166 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6824 (mm-40) REVERT: C 187 THR cc_start: 0.8127 (m) cc_final: 0.7890 (m) REVERT: D 71 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: E 145 MET cc_start: 0.2062 (OUTLIER) cc_final: 0.1768 (tmt) REVERT: E 163 MET cc_start: -0.0432 (mmp) cc_final: -0.0935 (tpp) REVERT: G 50 GLU cc_start: 0.8443 (pt0) cc_final: 0.7935 (pt0) REVERT: G 77 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: H 67 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7580 (mtm180) REVERT: L 21 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.6947 (pp20) REVERT: N 19 GLU cc_start: 0.6921 (mp0) cc_final: 0.6595 (mp0) REVERT: P 16 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8022 (p0) REVERT: Q 45 MET cc_start: 0.7595 (ttp) cc_final: 0.6940 (ttp) REVERT: Q 49 ASP cc_start: 0.7177 (m-30) cc_final: 0.6626 (m-30) outliers start: 62 outliers final: 33 residues processed: 453 average time/residue: 1.7555 time to fit residues: 904.3597 Evaluate side-chains 463 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 415 time to evaluate : 3.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 958 LYS Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 311 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 316 optimal weight: 7.9990 chunk 335 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 300 optimal weight: 0.2980 chunk 90 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 400 ASN B 582 ASN ** B 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 375 GLN D 75 HIS D 94 ASN G 6 GLN H 13 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 28495 Z= 0.227 Angle : 0.774 76.495 38458 Z= 0.331 Chirality : 0.047 0.763 4383 Planarity : 0.004 0.048 4927 Dihedral : 4.564 63.207 3884 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.23 % Allowed : 11.58 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3497 helix: 0.57 (0.15), residues: 1210 sheet: 0.00 (0.21), residues: 577 loop : -0.70 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 8 HIS 0.009 0.001 HIS A 426 PHE 0.017 0.002 PHE B 359 TYR 0.018 0.001 TYR A 850 ARG 0.008 0.000 ARG Y 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 425 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8050 (ptt) cc_final: 0.7628 (ptt) REVERT: A 200 LYS cc_start: 0.8393 (ptpp) cc_final: 0.8170 (pttm) REVERT: A 267 ASP cc_start: 0.7271 (m-30) cc_final: 0.6744 (t0) REVERT: A 346 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8024 (ttp) REVERT: A 359 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6536 (mp0) REVERT: A 363 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8447 (mm-40) REVERT: B 171 LEU cc_start: 0.8280 (mt) cc_final: 0.8045 (mt) REVERT: B 590 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6552 (mm-30) REVERT: B 594 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7899 (mttp) REVERT: B 599 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: B 770 LYS cc_start: 0.8016 (mttt) cc_final: 0.7685 (mttp) REVERT: B 835 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7578 (pt) REVERT: B 891 ASP cc_start: 0.7093 (m-30) cc_final: 0.6811 (m-30) REVERT: C 133 ASP cc_start: 0.6489 (m-30) cc_final: 0.6263 (m-30) REVERT: C 166 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6904 (tp40) REVERT: C 181 GLU cc_start: 0.6655 (pt0) cc_final: 0.6214 (pt0) REVERT: C 187 THR cc_start: 0.8200 (m) cc_final: 0.7979 (m) REVERT: D 71 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: E 69 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7042 (mm-30) REVERT: E 145 MET cc_start: 0.2266 (OUTLIER) cc_final: 0.1897 (tmt) REVERT: E 163 MET cc_start: -0.0335 (mmp) cc_final: -0.0716 (tpp) REVERT: G 50 GLU cc_start: 0.8397 (pt0) cc_final: 0.7891 (pt0) REVERT: G 77 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: H 67 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7537 (mtm180) REVERT: K 1 MET cc_start: 0.5314 (ttt) cc_final: 0.5001 (ttm) REVERT: L 21 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7006 (pp20) REVERT: N 19 GLU cc_start: 0.6896 (mp0) cc_final: 0.6578 (mp0) REVERT: P 12 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: P 16 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7988 (p0) REVERT: Q 45 MET cc_start: 0.7572 (ttp) cc_final: 0.6878 (ttp) REVERT: Q 49 ASP cc_start: 0.7207 (m-30) cc_final: 0.6731 (m-30) REVERT: Y 12 LYS cc_start: 0.6995 (ptpp) cc_final: 0.6703 (ptpp) REVERT: Y 77 LYS cc_start: 0.6852 (ttpt) cc_final: 0.6479 (pttp) outliers start: 69 outliers final: 39 residues processed: 455 average time/residue: 1.7486 time to fit residues: 904.4049 Evaluate side-chains 466 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 413 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 581 ASN Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 55 ILE Chi-restraints excluded: chain G residue 67 ASP Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 279 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 249 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN B 562 ASN B 582 ASN B 667 GLN B1009 GLN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 375 GLN D 75 HIS D 94 ASN G 6 GLN H 13 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.164 28495 Z= 0.461 Angle : 0.879 78.163 38458 Z= 0.393 Chirality : 0.053 0.640 4383 Planarity : 0.005 0.050 4927 Dihedral : 5.048 69.843 3884 Min Nonbonded Distance : 1.518 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.36 % Allowed : 12.88 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3497 helix: 0.24 (0.15), residues: 1208 sheet: -0.22 (0.21), residues: 590 loop : -0.85 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 8 HIS 0.010 0.002 HIS A 856 PHE 0.021 0.003 PHE B 359 TYR 0.026 0.002 TYR A 850 ARG 0.008 0.001 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 423 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8104 (ptt) cc_final: 0.7647 (ptt) REVERT: A 200 LYS cc_start: 0.8403 (ptpp) cc_final: 0.8190 (pttm) REVERT: A 267 ASP cc_start: 0.7387 (m-30) cc_final: 0.6860 (t0) REVERT: A 346 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8180 (ttp) REVERT: A 359 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: A 363 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8433 (mm-40) REVERT: B 197 GLN cc_start: 0.8291 (tt0) cc_final: 0.8079 (tt0) REVERT: B 594 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7966 (mttp) REVERT: B 599 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: B 617 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: B 1104 MET cc_start: 0.7930 (mtm) cc_final: 0.7628 (mtp) REVERT: C 133 ASP cc_start: 0.6594 (m-30) cc_final: 0.6373 (m-30) REVERT: C 161 MET cc_start: 0.7120 (mmp) cc_final: 0.6874 (mmp) REVERT: C 181 GLU cc_start: 0.6765 (pt0) cc_final: 0.6320 (pt0) REVERT: D 71 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: D 118 ASP cc_start: 0.8261 (t0) cc_final: 0.7897 (t0) REVERT: E 145 MET cc_start: 0.2286 (OUTLIER) cc_final: 0.1906 (tmt) REVERT: G 15 GLU cc_start: 0.6825 (mp0) cc_final: 0.6451 (mp0) REVERT: G 50 GLU cc_start: 0.8532 (pt0) cc_final: 0.7995 (pt0) REVERT: H 67 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7727 (mtm180) REVERT: K 1 MET cc_start: 0.5374 (ttt) cc_final: 0.5101 (ttm) REVERT: K 15 LYS cc_start: 0.7732 (tppt) cc_final: 0.7372 (ttmt) REVERT: K 77 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: L 21 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7148 (pp20) REVERT: N 19 GLU cc_start: 0.7068 (mp0) cc_final: 0.6673 (mp0) REVERT: P 12 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: P 16 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8064 (p0) REVERT: Q 45 MET cc_start: 0.7471 (ttp) cc_final: 0.6628 (ttp) REVERT: Q 49 ASP cc_start: 0.7276 (m-30) cc_final: 0.6781 (m-30) REVERT: Y 12 LYS cc_start: 0.6997 (ptpp) cc_final: 0.6676 (ptpt) REVERT: Y 77 LYS cc_start: 0.6933 (ttpt) cc_final: 0.6545 (pttp) outliers start: 73 outliers final: 40 residues processed: 461 average time/residue: 1.6976 time to fit residues: 892.2670 Evaluate side-chains 460 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 408 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 112 optimal weight: 2.9990 chunk 302 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 335 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN B 582 ASN B1009 GLN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 375 GLN D 75 HIS ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 28495 Z= 0.169 Angle : 0.757 77.164 38458 Z= 0.319 Chirality : 0.045 0.667 4383 Planarity : 0.004 0.050 4927 Dihedral : 4.500 64.045 3884 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.97 % Allowed : 13.81 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3497 helix: 0.63 (0.15), residues: 1200 sheet: -0.07 (0.21), residues: 591 loop : -0.70 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 8 HIS 0.005 0.001 HIS A 426 PHE 0.015 0.001 PHE B 359 TYR 0.013 0.001 TYR B 336 ARG 0.008 0.000 ARG Y 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 420 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8055 (ptt) cc_final: 0.7594 (ptt) REVERT: A 200 LYS cc_start: 0.8410 (ptpp) cc_final: 0.8196 (pttm) REVERT: A 267 ASP cc_start: 0.7236 (m-30) cc_final: 0.6713 (t0) REVERT: A 346 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8034 (ttp) REVERT: A 363 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8447 (mm-40) REVERT: B 171 LEU cc_start: 0.8215 (mt) cc_final: 0.7993 (mt) REVERT: B 255 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6779 (tt0) REVERT: B 458 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: B 594 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7638 (mttp) REVERT: B 599 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: B 770 LYS cc_start: 0.7992 (mttt) cc_final: 0.7474 (mttm) REVERT: B 835 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7528 (pt) REVERT: B 838 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7930 (mtt180) REVERT: B 995 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.7915 (mtt) REVERT: C 181 GLU cc_start: 0.6650 (pt0) cc_final: 0.6201 (pt0) REVERT: C 203 SER cc_start: 0.8098 (OUTLIER) cc_final: 0.7888 (t) REVERT: D 71 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: E 69 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7076 (mm-30) REVERT: E 145 MET cc_start: 0.2303 (OUTLIER) cc_final: 0.1948 (tmt) REVERT: G 77 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: K 1 MET cc_start: 0.5410 (ttt) cc_final: 0.5165 (ttm) REVERT: L 21 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.6920 (pp20) REVERT: N 19 GLU cc_start: 0.6909 (mp0) cc_final: 0.6569 (mp0) REVERT: P 12 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6940 (tt0) REVERT: Q 45 MET cc_start: 0.7439 (ttp) cc_final: 0.6703 (ttp) REVERT: Q 49 ASP cc_start: 0.7214 (m-30) cc_final: 0.6660 (m-30) REVERT: Y 12 LYS cc_start: 0.7029 (ptpp) cc_final: 0.6722 (ptpt) REVERT: Y 14 LYS cc_start: 0.6371 (ttmt) cc_final: 0.5995 (tttm) REVERT: Y 77 LYS cc_start: 0.6945 (ttpt) cc_final: 0.6576 (pttp) outliers start: 61 outliers final: 31 residues processed: 449 average time/residue: 1.7719 time to fit residues: 910.1588 Evaluate side-chains 453 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 409 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 ARG Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 206 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 323 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 282 optimal weight: 30.0000 chunk 187 optimal weight: 2.9990 chunk 334 optimal weight: 7.9990 chunk 209 optimal weight: 7.9990 chunk 203 optimal weight: 0.1980 chunk 154 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 400 ASN B 582 ASN B1009 GLN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN D 75 HIS D 94 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN L 78 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.166 28495 Z= 0.271 Angle : 0.800 78.566 38458 Z= 0.343 Chirality : 0.047 0.546 4383 Planarity : 0.004 0.050 4927 Dihedral : 4.645 64.229 3884 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.19 % Allowed : 14.36 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3497 helix: 0.54 (0.15), residues: 1210 sheet: -0.05 (0.21), residues: 579 loop : -0.72 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 8 HIS 0.008 0.001 HIS A 426 PHE 0.018 0.002 PHE B 359 TYR 0.021 0.002 TYR A 850 ARG 0.009 0.000 ARG Y 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 418 time to evaluate : 3.443 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.8068 (ptt) cc_final: 0.7590 (ptt) REVERT: A 200 LYS cc_start: 0.8422 (ptpp) cc_final: 0.8201 (pttm) REVERT: A 267 ASP cc_start: 0.7283 (m-30) cc_final: 0.6748 (t0) REVERT: A 346 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8080 (ttp) REVERT: A 359 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: A 363 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8467 (mm-40) REVERT: B 171 LEU cc_start: 0.8341 (mt) cc_final: 0.8119 (mt) REVERT: B 197 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: B 255 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6774 (tt0) REVERT: B 590 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6593 (mm-30) REVERT: B 594 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7650 (mttp) REVERT: B 599 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: B 617 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: B 770 LYS cc_start: 0.8081 (mttt) cc_final: 0.7559 (mttm) REVERT: B 835 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7613 (pt) REVERT: B 838 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7893 (mtt180) REVERT: B 995 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8291 (mtt) REVERT: C 161 MET cc_start: 0.6979 (mmp) cc_final: 0.5918 (mmt) REVERT: C 181 GLU cc_start: 0.6666 (pt0) cc_final: 0.6210 (pt0) REVERT: C 203 SER cc_start: 0.8213 (OUTLIER) cc_final: 0.7897 (t) REVERT: D 71 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: D 144 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7536 (mtp180) REVERT: E 101 MET cc_start: 0.1901 (mmt) cc_final: 0.1657 (mpp) REVERT: E 145 MET cc_start: 0.2404 (OUTLIER) cc_final: 0.2021 (tmt) REVERT: G 42 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: G 50 GLU cc_start: 0.8463 (pt0) cc_final: 0.7949 (pt0) REVERT: G 77 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: K 1 MET cc_start: 0.5414 (ttt) cc_final: 0.5179 (ttm) REVERT: K 77 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: L 21 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7048 (pp20) REVERT: N 19 GLU cc_start: 0.6943 (mp0) cc_final: 0.6567 (mp0) REVERT: N 57 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6644 (mmp80) REVERT: P 12 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7069 (tt0) REVERT: Q 45 MET cc_start: 0.7459 (ttp) cc_final: 0.6731 (ttp) REVERT: Q 49 ASP cc_start: 0.7227 (m-30) cc_final: 0.6743 (m-30) REVERT: Y 1 MET cc_start: 0.6981 (ttt) cc_final: 0.6735 (ttt) REVERT: Y 12 LYS cc_start: 0.7013 (ptpp) cc_final: 0.6718 (ptpt) REVERT: Y 14 LYS cc_start: 0.6392 (ttmt) cc_final: 0.6005 (tttm) REVERT: Y 77 LYS cc_start: 0.6945 (ttpt) cc_final: 0.6590 (pttp) outliers start: 68 outliers final: 35 residues processed: 453 average time/residue: 1.6711 time to fit residues: 863.3075 Evaluate side-chains 468 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 414 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 ARG Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 206 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN B 582 ASN B1009 GLN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 375 GLN D 75 HIS ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN L 78 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 28495 Z= 0.292 Angle : 0.810 78.431 38458 Z= 0.350 Chirality : 0.048 0.518 4383 Planarity : 0.005 0.050 4927 Dihedral : 4.707 64.695 3884 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.29 % Allowed : 14.59 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3497 helix: 0.50 (0.15), residues: 1211 sheet: -0.08 (0.21), residues: 581 loop : -0.74 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 8 HIS 0.006 0.001 HIS B 993 PHE 0.018 0.002 PHE B 359 TYR 0.021 0.002 TYR A 850 ARG 0.009 0.000 ARG Y 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 414 time to evaluate : 3.092 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.8066 (ptt) cc_final: 0.7617 (ptt) REVERT: A 200 LYS cc_start: 0.8422 (ptpp) cc_final: 0.8182 (pttm) REVERT: A 267 ASP cc_start: 0.7280 (m-30) cc_final: 0.6748 (t0) REVERT: A 346 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8100 (ttp) REVERT: A 359 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: A 363 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8467 (mm-40) REVERT: B 171 LEU cc_start: 0.8367 (mt) cc_final: 0.8130 (mt) REVERT: B 255 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6779 (tt0) REVERT: B 590 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6605 (mm-30) REVERT: B 594 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7672 (mttp) REVERT: B 599 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: B 617 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: B 759 GLU cc_start: 0.7778 (tt0) cc_final: 0.7554 (tt0) REVERT: B 770 LYS cc_start: 0.8110 (mttt) cc_final: 0.7581 (mttm) REVERT: B 835 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7640 (pt) REVERT: B 838 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7925 (mtt180) REVERT: B 995 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8284 (mtt) REVERT: C 181 GLU cc_start: 0.6673 (pt0) cc_final: 0.6216 (pt0) REVERT: C 203 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7907 (t) REVERT: D 71 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: D 144 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7557 (mtp180) REVERT: E 101 MET cc_start: 0.1844 (mmt) cc_final: 0.1577 (mpp) REVERT: E 145 MET cc_start: 0.2439 (OUTLIER) cc_final: 0.2041 (tmt) REVERT: G 42 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: G 50 GLU cc_start: 0.8469 (pt0) cc_final: 0.7942 (pt0) REVERT: G 77 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: H 67 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7596 (mtm180) REVERT: K 1 MET cc_start: 0.5424 (ttt) cc_final: 0.5200 (ttm) REVERT: K 15 LYS cc_start: 0.7673 (tppt) cc_final: 0.7270 (ttmt) REVERT: K 77 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: L 21 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7051 (pp20) REVERT: N 19 GLU cc_start: 0.6952 (mp0) cc_final: 0.6567 (mp0) REVERT: N 57 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6628 (mmp80) REVERT: P 12 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7075 (tt0) REVERT: Q 45 MET cc_start: 0.7460 (ttp) cc_final: 0.6727 (ttp) REVERT: Q 49 ASP cc_start: 0.7210 (m-30) cc_final: 0.6647 (m-30) REVERT: Y 1 MET cc_start: 0.6998 (ttt) cc_final: 0.6753 (ttt) REVERT: Y 12 LYS cc_start: 0.6982 (ptpp) cc_final: 0.6684 (ptpt) REVERT: Y 14 LYS cc_start: 0.6392 (ttmt) cc_final: 0.6008 (tttm) REVERT: Y 77 LYS cc_start: 0.6956 (ttpt) cc_final: 0.6584 (pttp) outliers start: 71 outliers final: 42 residues processed: 450 average time/residue: 1.7049 time to fit residues: 875.1747 Evaluate side-chains 474 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 413 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 ARG Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 304 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 311 optimal weight: 0.0040 chunk 187 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 310 optimal weight: 0.6980 overall best weight: 1.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 400 ASN B 582 ASN B1009 GLN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 375 GLN D 75 HIS D 94 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN L 78 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.166 28495 Z= 0.291 Angle : 0.795 74.362 38458 Z= 0.345 Chirality : 0.049 0.835 4383 Planarity : 0.005 0.050 4927 Dihedral : 4.717 65.065 3884 Min Nonbonded Distance : 1.540 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.13 % Allowed : 14.88 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3497 helix: 0.49 (0.15), residues: 1210 sheet: -0.07 (0.21), residues: 579 loop : -0.74 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 8 HIS 0.006 0.001 HIS B 993 PHE 0.018 0.002 PHE B 359 TYR 0.021 0.002 TYR A 850 ARG 0.009 0.000 ARG Y 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 417 time to evaluate : 3.648 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.8058 (ptt) cc_final: 0.7600 (ptt) REVERT: A 200 LYS cc_start: 0.8426 (ptpp) cc_final: 0.8183 (pttm) REVERT: A 267 ASP cc_start: 0.7275 (m-30) cc_final: 0.6747 (t0) REVERT: A 346 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8114 (ttp) REVERT: A 359 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6468 (mp0) REVERT: A 363 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8467 (mm-40) REVERT: B 171 LEU cc_start: 0.8368 (mt) cc_final: 0.8137 (mt) REVERT: B 255 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6781 (tt0) REVERT: B 458 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: B 590 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6595 (mm-30) REVERT: B 594 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7689 (mttp) REVERT: B 599 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: B 617 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: B 759 GLU cc_start: 0.7849 (tt0) cc_final: 0.7482 (tt0) REVERT: B 770 LYS cc_start: 0.8075 (mttt) cc_final: 0.7543 (mttm) REVERT: B 835 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7633 (pt) REVERT: B 838 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7918 (mtt180) REVERT: B 995 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8280 (mtt) REVERT: C 181 GLU cc_start: 0.6676 (pt0) cc_final: 0.6222 (pt0) REVERT: D 71 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: D 105 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: D 144 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7542 (mtp180) REVERT: E 101 MET cc_start: 0.2023 (mmt) cc_final: 0.1767 (mpp) REVERT: E 145 MET cc_start: 0.2408 (OUTLIER) cc_final: 0.2019 (tmt) REVERT: G 15 GLU cc_start: 0.6765 (mp0) cc_final: 0.6364 (mp0) REVERT: G 42 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: G 50 GLU cc_start: 0.8475 (pt0) cc_final: 0.7976 (pt0) REVERT: G 77 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: G 108 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8433 (mppt) REVERT: K 15 LYS cc_start: 0.7642 (tppt) cc_final: 0.7253 (ttmt) REVERT: K 77 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7029 (tt0) REVERT: L 21 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7056 (pp20) REVERT: N 19 GLU cc_start: 0.6958 (mp0) cc_final: 0.6562 (mp0) REVERT: N 57 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6654 (mmp80) REVERT: P 12 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: Q 45 MET cc_start: 0.7454 (ttp) cc_final: 0.6721 (ttp) REVERT: Q 49 ASP cc_start: 0.7210 (m-30) cc_final: 0.6638 (m-30) REVERT: Y 1 MET cc_start: 0.6995 (ttt) cc_final: 0.6753 (ttt) REVERT: Y 12 LYS cc_start: 0.6970 (ptpp) cc_final: 0.6657 (ptpt) REVERT: Y 14 LYS cc_start: 0.6417 (ttmt) cc_final: 0.6041 (tttm) REVERT: Y 77 LYS cc_start: 0.6947 (ttpt) cc_final: 0.6602 (pttp) outliers start: 66 outliers final: 43 residues processed: 449 average time/residue: 1.6713 time to fit residues: 854.7321 Evaluate side-chains 477 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 414 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 617 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 ARG Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 204 optimal weight: 0.5980 chunk 329 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 229 optimal weight: 8.9990 chunk 345 optimal weight: 0.9990 chunk 318 optimal weight: 1.9990 chunk 275 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 400 ASN B 582 ASN B1009 GLN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 375 GLN D 75 HIS D 94 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN L 78 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 28495 Z= 0.199 Angle : 0.680 78.547 38458 Z= 0.300 Chirality : 0.052 1.815 4383 Planarity : 0.004 0.050 4927 Dihedral : 4.385 62.168 3884 Min Nonbonded Distance : 1.582 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.74 % Allowed : 15.46 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3497 helix: 0.76 (0.16), residues: 1195 sheet: -0.02 (0.21), residues: 591 loop : -0.64 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 8 HIS 0.007 0.001 HIS A 426 PHE 0.014 0.001 PHE B 359 TYR 0.014 0.001 TYR B 336 ARG 0.009 0.000 ARG Y 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 421 time to evaluate : 3.347 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.8060 (ptt) cc_final: 0.7629 (ptt) REVERT: A 200 LYS cc_start: 0.8418 (ptpp) cc_final: 0.8172 (pttm) REVERT: A 208 ILE cc_start: 0.6396 (mm) cc_final: 0.6193 (mp) REVERT: A 267 ASP cc_start: 0.7194 (m-30) cc_final: 0.6692 (t0) REVERT: A 346 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8009 (ttp) REVERT: A 359 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: A 363 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8431 (mm-40) REVERT: B 171 LEU cc_start: 0.8215 (mt) cc_final: 0.7981 (mt) REVERT: B 255 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6787 (tt0) REVERT: B 458 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: B 590 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6599 (mm-30) REVERT: B 594 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7688 (mttp) REVERT: B 599 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: B 759 GLU cc_start: 0.7841 (tt0) cc_final: 0.7501 (tt0) REVERT: B 770 LYS cc_start: 0.8036 (mttt) cc_final: 0.7517 (mttm) REVERT: B 835 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7515 (pt) REVERT: B 838 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7860 (mtt180) REVERT: B 995 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.7937 (mtt) REVERT: C 161 MET cc_start: 0.7173 (mmp) cc_final: 0.5917 (mmt) REVERT: C 181 GLU cc_start: 0.6675 (pt0) cc_final: 0.6220 (pt0) REVERT: C 203 SER cc_start: 0.8169 (OUTLIER) cc_final: 0.7892 (t) REVERT: C 363 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7439 (mm-30) REVERT: D 71 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: D 144 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7513 (mtp180) REVERT: E 69 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7063 (mm-30) REVERT: E 101 MET cc_start: 0.2042 (mmt) cc_final: 0.1776 (tpp) REVERT: E 145 MET cc_start: 0.2656 (OUTLIER) cc_final: 0.2286 (tmt) REVERT: F 76 ILE cc_start: 0.1701 (mm) cc_final: 0.1439 (tp) REVERT: G 50 GLU cc_start: 0.8412 (pt0) cc_final: 0.7904 (pt0) REVERT: G 77 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: G 108 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8424 (mppt) REVERT: K 15 LYS cc_start: 0.7586 (tppt) cc_final: 0.7196 (ttmt) REVERT: K 77 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: L 21 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.6965 (pp20) REVERT: N 19 GLU cc_start: 0.6899 (mp0) cc_final: 0.6558 (mp0) REVERT: N 57 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.6522 (mmp80) REVERT: P 12 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: Q 45 MET cc_start: 0.7415 (ttp) cc_final: 0.7025 (ttm) REVERT: Q 49 ASP cc_start: 0.7182 (m-30) cc_final: 0.6643 (m-30) REVERT: Y 1 MET cc_start: 0.6965 (ttt) cc_final: 0.6734 (ttt) REVERT: Y 12 LYS cc_start: 0.6957 (ptpp) cc_final: 0.6651 (ptpt) REVERT: Y 14 LYS cc_start: 0.6397 (ttmt) cc_final: 0.6030 (tttm) REVERT: Y 77 LYS cc_start: 0.6956 (ttpt) cc_final: 0.6616 (pttp) outliers start: 54 outliers final: 32 residues processed: 445 average time/residue: 1.7436 time to fit residues: 884.9362 Evaluate side-chains 464 residues out of total 3115 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 414 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 788 ARG Chi-restraints excluded: chain B residue 835 ILE Chi-restraints excluded: chain B residue 838 ARG Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 995 MET Chi-restraints excluded: chain B residue 1086 VAL Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain N residue 57 ARG Chi-restraints excluded: chain P residue 12 GLU Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Y residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 347 random chunks: chunk 218 optimal weight: 7.9990 chunk 293 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 76 optimal weight: 0.0470 chunk 275 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 ASN B 562 ASN B 582 ASN B1009 GLN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN D 75 HIS D 94 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 13 ASN L 78 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.168122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107729 restraints weight = 25886.239| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.15 r_work: 0.3016 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 28495 Z= 0.267 Angle : 0.724 87.047 38458 Z= 0.324 Chirality : 0.050 1.319 4383 Planarity : 0.004 0.050 4927 Dihedral : 4.589 62.362 3884 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.87 % Allowed : 15.65 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3497 helix: 0.63 (0.15), residues: 1202 sheet: -0.03 (0.21), residues: 582 loop : -0.70 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 8 HIS 0.008 0.001 HIS A 426 PHE 0.018 0.002 PHE B 359 TYR 0.020 0.002 TYR A 850 ARG 0.009 0.000 ARG Y 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13372.25 seconds wall clock time: 237 minutes 26.40 seconds (14246.40 seconds total)