Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 11 10:37:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/07_2023/7nvx_12616_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/07_2023/7nvx_12616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/07_2023/7nvx_12616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/07_2023/7nvx_12616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/07_2023/7nvx_12616_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/07_2023/7nvx_12616_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.963 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: 10 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 52 5.49 5 Mg 1 5.21 5 S 146 5.16 5 Be 1 3.05 5 C 14929 2.51 5 N 4094 2.21 5 O 4426 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 114": "OE1" <-> "OE2" Residue "4 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 23663 Number of models: 1 Model: "" Number of chains: 18 Chain: "0" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5751 Classifications: {'peptide': 714} Link IDs: {'PTRANS': 32, 'TRANS': 681} Chain breaks: 1 Chain: "1" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2167 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 5 Chain: "2" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3158 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 369} Chain breaks: 4 Chain: "3" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1225 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "4" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2066 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 1 Chain: "5" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "6" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2567 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 310} Chain breaks: 1 Chain: "7" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4890 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Chain: "N" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 515 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "T" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 510 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "W" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" 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} Chain: "4" 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} Chain: "6" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1541 SG CYS 0 190 74.263 145.452 47.690 1.00 68.30 S ATOM 943 SG CYS 0 116 72.378 141.599 52.690 1.00 64.04 S ATOM 1083 SG CYS 0 134 68.335 142.945 48.031 1.00 54.22 S ATOM 1252 SG CYS 0 155 70.584 147.759 51.866 1.00 69.31 S ATOM 11119 SG CYS 3 6 21.227 127.727 50.470 1.00 69.65 S ATOM 11143 SG CYS 3 9 18.861 125.041 51.640 1.00 70.46 S ATOM 11315 SG CYS 3 31 20.904 124.607 48.427 1.00 69.70 S ATOM 11336 SG CYS 3 34 17.694 127.507 48.703 1.00 72.86 S ATOM 11280 SG CYS 3 26 20.767 137.691 43.295 1.00 63.49 S ATOM 11423 SG CYS 3 46 18.137 135.484 45.366 1.00 78.25 S ATOM 11445 SG CYS 3 49 19.533 138.727 46.595 1.00 76.89 S ATOM 14188 SG CYS 4 268 124.048 111.046 82.106 1.00 40.34 S ATOM 14207 SG CYS 4 271 127.151 110.811 79.826 1.00 42.66 S ATOM 14292 SG CYS 4 282 126.742 113.773 82.690 1.00 55.77 S ATOM 14312 SG CYS 4 285 124.509 113.626 79.171 1.00 50.77 S ATOM 14080 SG CYS 4 255 135.555 108.283 91.056 1.00 50.63 S ATOM 14097 SG CYS 4 257 135.030 111.991 89.311 1.00 53.68 S ATOM 14246 SG CYS 4 276 134.331 111.257 93.474 1.00 52.99 S ATOM 17135 SG CYS 6 345 131.364 83.832 59.631 1.00 33.62 S ATOM 17157 SG CYS 6 348 130.075 80.763 61.401 1.00 23.04 S ATOM 17314 SG CYS 6 368 127.737 82.971 59.433 1.00 31.55 S ATOM 17335 SG CYS 6 371 129.314 84.158 62.702 1.00 23.68 S ATOM 17255 SG CYS 6 360 132.282 95.212 61.839 1.00 49.29 S ATOM 17273 SG CYS 6 363 135.757 93.973 61.746 1.00 64.00 S ATOM 17422 SG CYS 6 382 132.882 92.831 64.382 1.00 38.31 S ATOM 17439 SG CYS 6 385 135.059 96.688 64.767 1.00 55.53 S ATOM 16699 SG CYS 6 291 120.278 101.540 101.547 1.00 33.57 S ATOM 16721 SG CYS 6 294 116.649 101.502 102.661 1.00 37.35 S ATOM 16810 SG CYS 6 305 117.496 102.193 99.050 1.00 45.15 S ATOM 16833 SG CYS 6 308 117.736 104.564 102.097 1.00 38.84 S Time building chain proxies: 11.55, per 1000 atoms: 0.49 Number of scatterers: 23663 At special positions: 0 Unit cell: (172.2, 170.1, 137.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 146 16.00 P 52 15.00 Mg 1 11.99 F 3 9.00 O 4426 8.00 N 4094 7.00 C 14929 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.93 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 01000 " pdb="FE1 SF4 01000 " - pdb=" SG CYS 0 190 " pdb="FE4 SF4 01000 " - pdb=" SG CYS 0 155 " pdb="FE3 SF4 01000 " - pdb=" SG CYS 0 134 " pdb="FE2 SF4 01000 " - pdb=" SG CYS 0 116 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 400 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 6 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 9 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 31 " pdb="ZN ZN 3 400 " - pdb=" SG CYS 3 34 " pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" NE2 HIS 3 28 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 49 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 46 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 26 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 268 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 271 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 285 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 282 " pdb=" ZN 4 402 " pdb="ZN ZN 4 402 " - pdb=" NE2 HIS 4 258 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 276 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 255 " pdb="ZN ZN 4 402 " - pdb=" SG CYS 4 257 " pdb=" ZN 6 401 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 345 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 348 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 371 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 368 " pdb=" ZN 6 402 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 360 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 382 " pdb="ZN ZN 6 402 " - pdb=" SG CYS 6 385 " pdb=" ZN 6 403 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 294 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 308 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 305 " pdb="ZN ZN 6 403 " - pdb=" SG CYS 6 291 " Number of angles added : 36 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 119 helices and 13 sheets defined 47.8% alpha, 6.7% beta 25 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 9.25 Creating SS restraints... Processing helix chain '0' and resid 19 through 34 Processing helix chain '0' and resid 48 through 62 removed outlier: 3.516A pdb=" N ILE 0 56 " --> pdb=" O LEU 0 52 " (cutoff:3.500A) Processing helix chain '0' and resid 77 through 98 removed outlier: 4.051A pdb=" N LYS 0 82 " --> pdb=" O PRO 0 78 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU 0 85 " --> pdb=" O GLU 0 81 " (cutoff:3.500A) Processing helix chain '0' and resid 119 through 122 No H-bonds generated for 'chain '0' and resid 119 through 122' Processing helix chain '0' and resid 127 through 137 Processing helix chain '0' and resid 140 through 148 removed outlier: 3.590A pdb=" N HIS 0 148 " --> pdb=" O ALA 0 144 " (cutoff:3.500A) Processing helix chain '0' and resid 156 through 164 removed outlier: 3.696A pdb=" N ALA 0 163 " --> pdb=" O GLU 0 159 " (cutoff:3.500A) Processing helix chain '0' and resid 177 through 187 Processing helix chain '0' and resid 191 through 201 removed outlier: 3.572A pdb=" N ALA 0 195 " --> pdb=" O PRO 0 191 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU 0 200 " --> pdb=" O ARG 0 196 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N HIS 0 201 " --> pdb=" O TYR 0 197 " (cutoff:3.500A) Processing helix chain '0' and resid 209 through 211 No H-bonds generated for 'chain '0' and resid 209 through 211' Processing helix chain '0' and resid 218 through 221 No H-bonds generated for 'chain '0' and resid 218 through 221' Processing helix chain '0' and resid 236 through 247 removed outlier: 3.583A pdb=" N ILE 0 239 " --> pdb=" O ALA 0 236 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP 0 240 " --> pdb=" O HIS 0 237 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN 0 241 " --> pdb=" O ASN 0 238 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE 0 244 " --> pdb=" O ASN 0 241 " (cutoff:3.500A) Processing helix chain '0' and resid 253 through 276 Processing helix chain '0' and resid 279 through 290 removed outlier: 4.422A pdb=" N GLU 0 284 " --> pdb=" O ARG 0 280 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR 0 285 " --> pdb=" O LEU 0 281 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG 0 286 " --> pdb=" O ARG 0 282 " (cutoff:3.500A) Processing helix chain '0' and resid 326 through 345 Processing helix chain '0' and resid 354 through 365 removed outlier: 4.546A pdb=" N LEU 0 358 " --> pdb=" O PRO 0 354 " (cutoff:3.500A) Processing helix chain '0' and resid 369 through 373 Processing helix chain '0' and resid 375 through 386 Processing helix chain '0' and resid 395 through 409 Processing helix chain '0' and resid 441 through 450 Proline residue: 0 446 - end of helix Processing helix chain '0' and resid 464 through 470 Proline residue: 0 468 - end of helix No H-bonds generated for 'chain '0' and resid 464 through 470' Processing helix chain '0' and resid 514 through 530 removed outlier: 3.605A pdb=" N VAL 0 530 " --> pdb=" O GLU 0 526 " (cutoff:3.500A) Processing helix chain '0' and resid 542 through 554 Processing helix chain '0' and resid 557 through 564 Processing helix chain '0' and resid 574 through 589 Processing helix chain '0' and resid 603 through 607 Processing helix chain '0' and resid 631 through 642 Processing helix chain '0' and resid 648 through 668 removed outlier: 4.460A pdb=" N ARG 0 666 " --> pdb=" O GLN 0 662 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA 0 667 " --> pdb=" O CYS 0 663 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE 0 668 " --> pdb=" O VAL 0 664 " (cutoff:3.500A) Processing helix chain '0' and resid 687 through 692 Processing helix chain '0' and resid 695 through 700 removed outlier: 3.599A pdb=" N HIS 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 710 through 725 Processing helix chain '1' and resid 109 through 119 removed outlier: 4.335A pdb=" N GLN 1 119 " --> pdb=" O ASN 1 115 " (cutoff:3.500A) Processing helix chain '1' and resid 122 through 133 removed outlier: 3.505A pdb=" N LEU 1 127 " --> pdb=" O VAL 1 123 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR 1 128 " --> pdb=" O LEU 1 124 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL 1 132 " --> pdb=" O TYR 1 128 " (cutoff:3.500A) Processing helix chain '1' and resid 140 through 145 Processing helix chain '1' and resid 191 through 199 Processing helix chain '1' and resid 201 through 209 Processing helix chain '1' and resid 217 through 225 removed outlier: 3.537A pdb=" N PHE 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE 1 225 " --> pdb=" O TRP 1 221 " (cutoff:3.500A) Processing helix chain '1' and resid 298 through 317 removed outlier: 3.539A pdb=" N ALA 1 302 " --> pdb=" O ASN 1 298 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE 1 303 " --> pdb=" O SER 1 299 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE 1 304 " --> pdb=" O ASN 1 300 " (cutoff:3.500A) Processing helix chain '1' and resid 380 through 383 No H-bonds generated for 'chain '1' and resid 380 through 383' Processing helix chain '1' and resid 397 through 408 removed outlier: 3.512A pdb=" N ILE 1 401 " --> pdb=" O SER 1 397 " (cutoff:3.500A) Processing helix chain '1' and resid 424 through 434 Processing helix chain '1' and resid 456 through 479 removed outlier: 3.979A pdb=" N GLU 1 460 " --> pdb=" O ASP 1 456 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N HIS 1 474 " --> pdb=" O GLU 1 470 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS 1 478 " --> pdb=" O HIS 1 474 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE 1 479 " --> pdb=" O PHE 1 475 " (cutoff:3.500A) Processing helix chain '1' and resid 486 through 514 removed outlier: 3.751A pdb=" N VAL 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS 1 492 " --> pdb=" O GLU 1 488 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE 1 500 " --> pdb=" O ASN 1 496 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU 1 505 " --> pdb=" O GLN 1 501 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS 1 506 " --> pdb=" O VAL 1 502 " (cutoff:3.500A) Proline residue: 1 507 - end of helix Processing helix chain '1' and resid 524 through 546 removed outlier: 3.608A pdb=" N MET 1 528 " --> pdb=" O HIS 1 524 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU 1 529 " --> pdb=" O ILE 1 525 " (cutoff:3.500A) Processing helix chain '2' and resid 19 through 24 Processing helix chain '2' and resid 28 through 34 Processing helix chain '2' and resid 38 through 46 Processing helix chain '2' and resid 51 through 60 Processing helix chain '2' and resid 68 through 74 Processing helix chain '2' and resid 80 through 93 Processing helix chain '2' and resid 112 through 121 Processing helix chain '2' and resid 146 through 163 removed outlier: 3.532A pdb=" N LYS 2 150 " --> pdb=" O PRO 2 146 " (cutoff:3.500A) Processing helix chain '2' and resid 173 through 181 Processing helix chain '2' and resid 198 through 205 removed outlier: 3.743A pdb=" N GLN 2 202 " --> pdb=" O SER 2 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU 2 205 " --> pdb=" O PHE 2 201 " (cutoff:3.500A) Processing helix chain '2' and resid 208 through 226 removed outlier: 3.780A pdb=" N GLN 2 224 " --> pdb=" O LEU 2 220 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER 2 225 " --> pdb=" O GLN 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 230 through 241 Processing helix chain '2' and resid 256 through 268 Processing helix chain '2' and resid 285 through 288 No H-bonds generated for 'chain '2' and resid 285 through 288' Processing helix chain '2' and resid 322 through 330 Processing helix chain '2' and resid 348 through 357 Processing helix chain '2' and resid 361 through 370 Processing helix chain '2' and resid 374 through 378 removed outlier: 3.910A pdb=" N LYS 2 378 " --> pdb=" O PRO 2 374 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 374 through 378' Processing helix chain '2' and resid 385 through 398 removed outlier: 3.781A pdb=" N ARG 2 398 " --> pdb=" O TRP 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 415 through 428 removed outlier: 3.713A pdb=" N GLU 2 419 " --> pdb=" O GLN 2 415 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU 2 420 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing helix chain '2' and resid 445 through 457 removed outlier: 4.506A pdb=" N SER 2 449 " --> pdb=" O ALA 2 446 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 15 No H-bonds generated for 'chain '3' and resid 12 through 15' Processing helix chain '3' and resid 32 through 40 removed outlier: 3.635A pdb=" N LEU 3 37 " --> pdb=" O SER 3 33 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 80 removed outlier: 3.519A pdb=" N LYS 3 70 " --> pdb=" O PRO 3 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS 3 77 " --> pdb=" O GLU 3 73 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS 3 80 " --> pdb=" O LYS 3 76 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 88 No H-bonds generated for 'chain '3' and resid 86 through 88' Processing helix chain '3' and resid 93 through 110 removed outlier: 3.822A pdb=" N ASN 3 96 " --> pdb=" O ARG 3 93 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE 3 98 " --> pdb=" O TYR 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 114 through 128 removed outlier: 3.847A pdb=" N LYS 3 127 " --> pdb=" O GLU 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 148 removed outlier: 4.177A pdb=" N THR 3 141 " --> pdb=" O LYS 3 137 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG 3 142 " --> pdb=" O LEU 3 138 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 28 Processing helix chain '4' and resid 34 through 51 Processing helix chain '4' and resid 102 through 120 Processing helix chain '4' and resid 134 through 150 Processing helix chain '4' and resid 171 through 187 removed outlier: 4.923A pdb=" N MET 4 175 " --> pdb=" O LEU 4 172 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN 4 176 " --> pdb=" O GLN 4 173 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE 4 181 " --> pdb=" O MET 4 178 " (cutoff:3.500A) Processing helix chain '4' and resid 201 through 209 removed outlier: 3.750A pdb=" N ASP 4 208 " --> pdb=" O GLN 4 204 " (cutoff:3.500A) Processing helix chain '4' and resid 220 through 230 removed outlier: 4.859A pdb=" N LEU 4 224 " --> pdb=" O PRO 4 221 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU 4 228 " --> pdb=" O GLN 4 225 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL 4 230 " --> pdb=" O LEU 4 227 " (cutoff:3.500A) Processing helix chain '4' and resid 235 through 238 No H-bonds generated for 'chain '4' and resid 235 through 238' Processing helix chain '5' and resid 14 through 26 removed outlier: 3.545A pdb=" N GLN 5 18 " --> pdb=" O PRO 5 14 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE 5 19 " --> pdb=" O ALA 5 15 " (cutoff:3.500A) Processing helix chain '5' and resid 50 through 63 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 80 through 98 removed outlier: 3.654A pdb=" N TYR 6 90 " --> pdb=" O LYS 6 86 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE 6 96 " --> pdb=" O VAL 6 92 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP 6 97 " --> pdb=" O GLU 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 124 through 136 removed outlier: 4.516A pdb=" N ASP 6 136 " --> pdb=" O LYS 6 132 " (cutoff:3.500A) Processing helix chain '6' and resid 145 through 158 removed outlier: 4.198A pdb=" N HIS 6 158 " --> pdb=" O GLN 6 154 " (cutoff:3.500A) Processing helix chain '6' and resid 183 through 191 Processing helix chain '6' and resid 206 through 215 Processing helix chain '6' and resid 225 through 236 removed outlier: 3.694A pdb=" N GLU 6 230 " --> pdb=" O SER 6 226 " (cutoff:3.500A) Processing helix chain '6' and resid 315 through 325 removed outlier: 3.869A pdb=" N SER 6 321 " --> pdb=" O HIS 6 317 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR 6 322 " --> pdb=" O LEU 6 318 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N HIS 6 323 " --> pdb=" O ALA 6 319 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N HIS 6 324 " --> pdb=" O ARG 6 320 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU 6 325 " --> pdb=" O SER 6 321 " (cutoff:3.500A) Processing helix chain '6' and resid 369 through 377 Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '7' and resid 93 through 103 removed outlier: 3.557A pdb=" N ASP 7 98 " --> pdb=" O LYS 7 94 " (cutoff:3.500A) Processing helix chain '7' and resid 120 through 129 removed outlier: 3.672A pdb=" N ALA 7 126 " --> pdb=" O SER 7 122 " (cutoff:3.500A) Processing helix chain '7' and resid 133 through 143 Processing helix chain '7' and resid 150 through 160 removed outlier: 3.585A pdb=" N THR 7 160 " --> pdb=" O ILE 7 156 " (cutoff:3.500A) Processing helix chain '7' and resid 182 through 190 Processing helix chain '7' and resid 192 through 196 Processing helix chain '7' and resid 274 through 286 removed outlier: 5.068A pdb=" N GLU 7 278 " --> pdb=" O GLU 7 275 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU 7 279 " --> pdb=" O MET 7 276 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE 7 285 " --> pdb=" O LYS 7 282 " (cutoff:3.500A) Processing helix chain '7' and resid 297 through 299 No H-bonds generated for 'chain '7' and resid 297 through 299' Processing helix chain '7' and resid 318 through 327 Processing helix chain '7' and resid 346 through 357 Processing helix chain '7' and resid 368 through 381 Processing helix chain '7' and resid 410 through 414 Processing helix chain '7' and resid 421 through 431 removed outlier: 3.771A pdb=" N VAL 7 426 " --> pdb=" O GLU 7 422 " (cutoff:3.500A) Processing helix chain '7' and resid 443 through 445 No H-bonds generated for 'chain '7' and resid 443 through 445' Processing helix chain '7' and resid 451 through 457 removed outlier: 3.524A pdb=" N ILE 7 457 " --> pdb=" O VAL 7 454 " (cutoff:3.500A) Processing helix chain '7' and resid 476 through 483 removed outlier: 3.707A pdb=" N LEU 7 483 " --> pdb=" O LEU 7 480 " (cutoff:3.500A) Processing helix chain '7' and resid 493 through 499 Processing helix chain '7' and resid 516 through 524 removed outlier: 3.644A pdb=" N GLU 7 521 " --> pdb=" O GLU 7 517 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA 7 524 " --> pdb=" O ARG 7 520 " (cutoff:3.500A) Processing helix chain '7' and resid 530 through 535 Processing helix chain '7' and resid 538 through 554 Processing helix chain '7' and resid 565 through 575 Processing helix chain '7' and resid 586 through 598 Processing helix chain '7' and resid 609 through 612 removed outlier: 3.698A pdb=" N ASP 7 612 " --> pdb=" O LYS 7 609 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 609 through 612' Processing helix chain '7' and resid 633 through 644 removed outlier: 3.770A pdb=" N ARG 7 642 " --> pdb=" O GLN 7 638 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL 7 643 " --> pdb=" O ARG 7 639 " (cutoff:3.500A) Processing helix chain '7' and resid 668 through 683 removed outlier: 3.682A pdb=" N ARG 7 678 " --> pdb=" O THR 7 674 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE 7 679 " --> pdb=" O LYS 7 675 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU 7 680 " --> pdb=" O ARG 7 676 " (cutoff:3.500A) Processing helix chain '7' and resid 706 through 719 Processing helix chain 'W' and resid 279 through 282 No H-bonds generated for 'chain 'W' and resid 279 through 282' Processing sheet with id= A, first strand: chain '0' and resid 478 through 480 removed outlier: 7.355A pdb=" N VAL 0 39 " --> pdb=" O ALA 0 479 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL 0 231 " --> pdb=" O SER 0 453 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '0' and resid 173 through 175 removed outlier: 4.124A pdb=" N ALA 0 108 " --> pdb=" O TYR 0 175 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL 0 204 " --> pdb=" O LEU 0 107 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '0' and resid 250 through 252 removed outlier: 3.538A pdb=" N ILE 0 432 " --> pdb=" O GLU 0 419 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '0' and resid 490 through 494 removed outlier: 7.672A pdb=" N GLY 0 675 " --> pdb=" O CYS 0 491 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N MET 0 493 " --> pdb=" O GLY 0 675 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N MET 0 677 " --> pdb=" O MET 0 493 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL 0 536 " --> pdb=" O ALA 0 617 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU 0 566 " --> pdb=" O ILE 0 595 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU 0 597 " --> pdb=" O LEU 0 566 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE 0 568 " --> pdb=" O LEU 0 597 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N VAL 0 599 " --> pdb=" O PHE 0 568 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 307 through 309 removed outlier: 6.574A pdb=" N GLN 2 345 " --> pdb=" O MET 2 334 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N MET 2 334 " --> pdb=" O GLN 2 345 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 407 through 409 removed outlier: 3.880A pdb=" N MET 2 441 " --> pdb=" O TYR 2 409 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE 2 433 " --> pdb=" O VAL 2 442 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '4' and resid 10 through 14 removed outlier: 6.837A pdb=" N LYS 4 56 " --> pdb=" O LEU 4 11 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N ILE 4 13 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA 4 58 " --> pdb=" O ILE 4 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain '5' and resid 8 through 11 removed outlier: 3.654A pdb=" N PHE 5 44 " --> pdb=" O GLN 5 36 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN 5 36 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '6' and resid 164 through 170 removed outlier: 3.524A pdb=" N ASP 6 66 " --> pdb=" O ILE 6 170 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN 6 103 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL 6 63 " --> pdb=" O GLN 6 103 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLY 6 105 " --> pdb=" O VAL 6 63 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL 6 65 " --> pdb=" O GLY 6 105 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE 6 107 " --> pdb=" O VAL 6 65 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '7' and resid 76 through 78 removed outlier: 6.071A pdb=" N LYS 7 117 " --> pdb=" O PRO 7 106 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '7' and resid 167 through 171 removed outlier: 4.179A pdb=" N TYR 7 175 " --> pdb=" O VAL 7 272 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE 7 270 " --> pdb=" O VAL 7 177 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER 7 179 " --> pdb=" O VAL 7 268 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '7' and resid 389 through 392 removed outlier: 6.748A pdb=" N VAL 7 405 " --> pdb=" O CYS 7 390 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE 7 392 " --> pdb=" O VAL 7 405 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE 7 407 " --> pdb=" O PHE 7 392 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS 7 361 " --> pdb=" O ALA 7 406 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N SER 7 408 " --> pdb=" O CYS 7 361 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL 7 363 " --> pdb=" O SER 7 408 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU 7 437 " --> pdb=" O LEU 7 362 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU 7 364 " --> pdb=" O LEU 7 437 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE 7 439 " --> pdb=" O LEU 7 364 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N CYS 7 462 " --> pdb=" O MET 7 438 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU 7 440 " --> pdb=" O CYS 7 462 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU 7 464 " --> pdb=" O LEU 7 440 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY 7 336 " --> pdb=" O GLY 7 465 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N THR 7 467 " --> pdb=" O GLY 7 336 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE 7 338 " --> pdb=" O THR 7 467 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL 7 339 " --> pdb=" O LEU 7 488 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU 7 490 " --> pdb=" O VAL 7 339 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '7' and resid 688 through 690 removed outlier: 3.559A pdb=" N LYS 7 688 " --> pdb=" O CYS 7 507 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA 7 657 " --> pdb=" O GLN 7 506 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ALA 7 508 " --> pdb=" O ALA 7 657 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE 7 659 " --> pdb=" O ALA 7 508 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL 7 510 " --> pdb=" O PHE 7 659 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER 7 661 " --> pdb=" O VAL 7 510 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2361 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 8.35 Time building geometry restraints manager: 11.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10168 1.43 - 1.64: 13848 1.64 - 1.86: 214 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 24242 Sorted by residual: bond pdb=" C4 ADP 7 901 " pdb=" C5 ADP 7 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" BE BEF 7 903 " pdb=" F2 BEF 7 903 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C5 ADP 7 901 " pdb=" C6 ADP 7 901 " ideal model delta sigma weight residual 1.490 1.409 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" BE BEF 7 903 " pdb=" F3 BEF 7 903 " ideal model delta sigma weight residual 1.476 1.547 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" BE BEF 7 903 " pdb=" F1 BEF 7 903 " ideal model delta sigma weight residual 1.476 1.532 -0.056 2.00e-02 2.50e+03 7.88e+00 ... (remaining 24237 not shown) Histogram of bond angle deviations from ideal: 73.38 - 85.51: 12 85.51 - 97.63: 0 97.63 - 109.76: 2974 109.76 - 121.89: 25179 121.89 - 134.02: 4836 Bond angle restraints: 33001 Sorted by residual: angle pdb=" PA ADP 7 901 " pdb=" O3A ADP 7 901 " pdb=" PB ADP 7 901 " ideal model delta sigma weight residual 120.50 131.95 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C2' ADP 7 901 " pdb=" C3' ADP 7 901 " pdb=" C4' ADP 7 901 " ideal model delta sigma weight residual 111.00 100.09 10.91 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C1' ADP 7 901 " pdb=" C2' ADP 7 901 " pdb=" C3' ADP 7 901 " ideal model delta sigma weight residual 111.00 100.13 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" N ILE 5 35 " pdb=" CA ILE 5 35 " pdb=" C ILE 5 35 " ideal model delta sigma weight residual 111.90 109.21 2.69 8.10e-01 1.52e+00 1.10e+01 angle pdb=" C SER 0 462 " pdb=" CA SER 0 462 " pdb=" CB SER 0 462 " ideal model delta sigma weight residual 109.51 115.52 -6.01 1.85e+00 2.92e-01 1.06e+01 ... (remaining 32996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 13443 24.09 - 48.18: 935 48.18 - 72.27: 135 72.27 - 96.36: 18 96.36 - 120.45: 1 Dihedral angle restraints: 14532 sinusoidal: 6247 harmonic: 8285 Sorted by residual: dihedral pdb=" C5' ADP 7 901 " pdb=" O5' ADP 7 901 " pdb=" PA ADP 7 901 " pdb=" O2A ADP 7 901 " ideal model delta sinusoidal sigma weight residual 300.00 179.55 120.45 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" CA GLY 3 27 " pdb=" C GLY 3 27 " pdb=" N HIS 3 28 " pdb=" CA HIS 3 28 " ideal model delta harmonic sigma weight residual 180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA SER 0 462 " pdb=" C SER 0 462 " pdb=" N PRO 0 463 " pdb=" CA PRO 0 463 " ideal model delta harmonic sigma weight residual 180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 14529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2989 0.041 - 0.081: 506 0.081 - 0.122: 215 0.122 - 0.162: 13 0.162 - 0.203: 1 Chirality restraints: 3724 Sorted by residual: chirality pdb=" C3' ADP 7 901 " pdb=" C2' ADP 7 901 " pdb=" C4' ADP 7 901 " pdb=" O3' ADP 7 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE 7 580 " pdb=" N ILE 7 580 " pdb=" C ILE 7 580 " pdb=" CB ILE 7 580 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL 1 211 " pdb=" N VAL 1 211 " pdb=" C VAL 1 211 " pdb=" CB VAL 1 211 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 3721 not shown) Planarity restraints: 4029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER 0 462 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO 0 463 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO 0 463 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO 0 463 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE 2 338 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.29e+00 pdb=" N PRO 2 339 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO 2 339 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO 2 339 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP 2 96 " 0.011 2.00e-02 2.50e+03 8.87e-03 1.97e+00 pdb=" CG TRP 2 96 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP 2 96 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP 2 96 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP 2 96 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP 2 96 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP 2 96 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP 2 96 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP 2 96 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP 2 96 " -0.000 2.00e-02 2.50e+03 ... (remaining 4026 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 225 2.56 - 3.14: 20377 3.14 - 3.73: 38383 3.73 - 4.31: 52018 4.31 - 4.90: 85121 Nonbonded interactions: 196124 Sorted by model distance: nonbonded pdb=" OE2 GLU 7 442 " pdb=" OG SER 7 614 " model vdw 1.971 2.440 nonbonded pdb=" O GLU 1 527 " pdb=" OG1 THR 1 531 " model vdw 1.990 2.440 nonbonded pdb=" O2B ADP 7 901 " pdb="MG MG 7 902 " model vdw 2.001 2.170 nonbonded pdb=" O PHE 7 378 " pdb=" OG SER 7 382 " model vdw 2.011 2.440 nonbonded pdb=" OG SER 2 172 " pdb=" OD1 ASP 2 174 " model vdw 2.013 2.440 ... (remaining 196119 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 20.210 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 75.680 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.109 24242 Z= 0.164 Angle : 0.492 11.446 33001 Z= 0.275 Chirality : 0.037 0.203 3724 Planarity : 0.003 0.058 4029 Dihedral : 15.653 120.451 9148 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.85 (0.17), residues: 2752 helix: 2.06 (0.15), residues: 1293 sheet: -1.28 (0.31), residues: 311 loop : -0.61 (0.18), residues: 1148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 689 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 689 average time/residue: 0.3932 time to fit residues: 406.3072 Evaluate side-chains 408 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 3.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 0.5980 chunk 212 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 143 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 219 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 328 HIS ** 0 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 384 HIS ** 0 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 649 ASN ** 1 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 289 ASN 2 424 HIS 3 24 ASN ** 3 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 176 ASN ** 5 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 97 GLN 7 459 GLN 7 481 ASN ** 7 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 564 ASN 7 595 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 24242 Z= 0.266 Angle : 0.666 11.315 33001 Z= 0.342 Chirality : 0.043 0.244 3724 Planarity : 0.005 0.086 4029 Dihedral : 12.628 78.687 3570 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.43 % Favored : 95.53 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.21 (0.16), residues: 2752 helix: 1.27 (0.14), residues: 1329 sheet: -1.20 (0.31), residues: 308 loop : -0.79 (0.18), residues: 1115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 440 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 43 residues processed: 480 average time/residue: 0.3583 time to fit residues: 272.8164 Evaluate side-chains 389 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 346 time to evaluate : 2.863 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2312 time to fit residues: 22.1250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 211 optimal weight: 0.0980 chunk 173 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 348 HIS ** 0 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 224 GLN ** 3 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 63 GLN 7 187 HIS 7 459 GLN 7 506 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 24242 Z= 0.330 Angle : 0.672 11.169 33001 Z= 0.343 Chirality : 0.043 0.165 3724 Planarity : 0.005 0.066 4029 Dihedral : 13.045 69.625 3570 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.80 % Favored : 95.17 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.32 (0.16), residues: 2752 helix: 0.77 (0.14), residues: 1339 sheet: -1.53 (0.33), residues: 264 loop : -1.00 (0.18), residues: 1149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 375 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 25 residues processed: 409 average time/residue: 0.3490 time to fit residues: 225.7775 Evaluate side-chains 342 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 317 time to evaluate : 2.727 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2361 time to fit residues: 14.2001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 1.9990 chunk 191 optimal weight: 0.2980 chunk 132 optimal weight: 6.9990 chunk 28 optimal weight: 0.3980 chunk 121 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 255 optimal weight: 0.0870 chunk 270 optimal weight: 0.0870 chunk 133 optimal weight: 0.9980 chunk 242 optimal weight: 0.1980 chunk 72 optimal weight: 5.9990 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 135 HIS ** 0 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 37 HIS ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 GLN ** 3 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 145 HIS ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 173 ASN 7 481 ASN 7 506 GLN 7 656 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 24242 Z= 0.172 Angle : 0.610 9.791 33001 Z= 0.306 Chirality : 0.041 0.182 3724 Planarity : 0.004 0.048 4029 Dihedral : 13.012 69.675 3570 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2752 helix: 0.80 (0.14), residues: 1333 sheet: -1.37 (0.32), residues: 278 loop : -1.02 (0.18), residues: 1141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 417 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 20 residues processed: 444 average time/residue: 0.3522 time to fit residues: 247.2112 Evaluate side-chains 366 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 346 time to evaluate : 2.819 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2213 time to fit residues: 12.2236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 201 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 230 optimal weight: 0.1980 chunk 187 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 242 optimal weight: 0.0970 chunk 68 optimal weight: 0.4980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 37 HIS ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 224 GLN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 187 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 24242 Z= 0.198 Angle : 0.607 11.482 33001 Z= 0.304 Chirality : 0.041 0.192 3724 Planarity : 0.004 0.054 4029 Dihedral : 13.054 70.218 3570 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.57 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2752 helix: 0.74 (0.14), residues: 1335 sheet: -1.34 (0.32), residues: 266 loop : -1.03 (0.18), residues: 1151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 366 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 395 average time/residue: 0.3602 time to fit residues: 225.4188 Evaluate side-chains 344 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 325 time to evaluate : 2.793 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2137 time to fit residues: 11.5013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 9.9990 chunk 243 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 270 optimal weight: 0.7980 chunk 224 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 519 ASN 1 398 GLN 2 37 HIS ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 364 GLN 7 187 HIS 7 710 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 24242 Z= 0.245 Angle : 0.642 12.940 33001 Z= 0.319 Chirality : 0.042 0.235 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.228 70.752 3570 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.28 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.49 (0.16), residues: 2752 helix: 0.66 (0.14), residues: 1339 sheet: -1.53 (0.31), residues: 274 loop : -1.12 (0.18), residues: 1139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 344 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 21 residues processed: 375 average time/residue: 0.3679 time to fit residues: 216.5505 Evaluate side-chains 341 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 320 time to evaluate : 2.776 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2331 time to fit residues: 12.8155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 228 optimal weight: 0.4980 chunk 151 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 164 optimal weight: 0.6980 chunk 124 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN ** 4 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 24242 Z= 0.218 Angle : 0.630 11.999 33001 Z= 0.313 Chirality : 0.041 0.178 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.243 71.362 3570 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.53 (0.16), residues: 2752 helix: 0.65 (0.14), residues: 1347 sheet: -1.53 (0.31), residues: 274 loop : -1.20 (0.18), residues: 1131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 352 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 372 average time/residue: 0.3689 time to fit residues: 219.3935 Evaluate side-chains 338 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 324 time to evaluate : 2.915 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2254 time to fit residues: 9.7401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 171 optimal weight: 0.1980 chunk 183 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 555 GLN ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 362 GLN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 54 GLN ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 364 GLN ** 7 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 190 GLN ** 7 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 24242 Z= 0.268 Angle : 0.670 15.278 33001 Z= 0.334 Chirality : 0.042 0.228 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.343 71.565 3570 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.61 (0.16), residues: 2752 helix: 0.57 (0.14), residues: 1340 sheet: -1.68 (0.31), residues: 275 loop : -1.18 (0.18), residues: 1137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 331 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 351 average time/residue: 0.3458 time to fit residues: 193.1240 Evaluate side-chains 335 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 319 time to evaluate : 2.705 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2428 time to fit residues: 10.6379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 227 optimal weight: 0.8980 chunk 237 optimal weight: 0.9980 chunk 250 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 0 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 187 GLN ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 24 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN ** 4 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 24242 Z= 0.260 Angle : 0.663 14.320 33001 Z= 0.332 Chirality : 0.042 0.225 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.365 71.712 3570 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.23 % Favored : 94.73 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.70 (0.16), residues: 2752 helix: 0.54 (0.14), residues: 1340 sheet: -1.82 (0.31), residues: 275 loop : -1.26 (0.18), residues: 1137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 344 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 352 average time/residue: 0.3554 time to fit residues: 198.8750 Evaluate side-chains 322 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 316 time to evaluate : 2.647 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2113 time to fit residues: 6.1886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 0.6980 chunk 265 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 278 optimal weight: 0.0050 chunk 256 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 171 optimal weight: 0.0370 chunk 136 optimal weight: 8.9990 overall best weight: 0.4472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 24 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 9 ASN 4 48 HIS ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 24242 Z= 0.206 Angle : 0.656 13.578 33001 Z= 0.326 Chirality : 0.042 0.255 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.266 72.364 3570 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.61 (0.16), residues: 2752 helix: 0.62 (0.14), residues: 1335 sheet: -1.70 (0.30), residues: 278 loop : -1.23 (0.18), residues: 1139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 350 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 354 average time/residue: 0.3813 time to fit residues: 216.3420 Evaluate side-chains 335 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 329 time to evaluate : 2.801 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2273 time to fit residues: 6.3866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 0.8980 chunk 236 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 204 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 222 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 228 optimal weight: 0.0270 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 20 GLN ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 48 HIS 4 205 GLN ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 376 HIS ** 7 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 481 ASN ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.174900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.153195 restraints weight = 44549.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.150597 restraints weight = 65818.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.148909 restraints weight = 54267.071| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 24242 Z= 0.231 Angle : 0.673 13.421 33001 Z= 0.334 Chirality : 0.043 0.245 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.309 72.844 3570 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.12 % Favored : 94.84 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.66 (0.16), residues: 2752 helix: 0.56 (0.14), residues: 1341 sheet: -1.74 (0.30), residues: 279 loop : -1.24 (0.18), residues: 1132 =============================================================================== Job complete usr+sys time: 5116.17 seconds wall clock time: 94 minutes 46.66 seconds (5686.66 seconds total)