Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 11 19:18:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/10_2023/7nvx_12616_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/10_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_12616/10_2023/7nvx_12616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/10_2023/7nvx_12616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/10_2023/7nvx_12616_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/10_2023/7nvx_12616_updated.pdb" } resolution = 3.9 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= -0.002 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-1.21rc1-5097/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: 12.13, per 1000 atoms: 0.51 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: 10.01 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: 10.26 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: 8.76 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: 1.22 - 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: 4.880 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: 0.020 Extract box with map and model: 19.830 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 76.100 Find NCS groups from input model: 0.710 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.000 ------------------------------------------------------------------------------- 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 % Allowed : 0.20 % Favored : 99.80 % 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 : 2.474 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: 0.3917 time to fit residues: 406.0288 Evaluate side-chains 408 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 2.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8432 ------------------------------------------------------------------------------- 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 ** 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: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24242 Z= 0.268 Angle : 0.665 11.274 33001 Z= 0.342 Chirality : 0.043 0.236 3724 Planarity : 0.005 0.090 4029 Dihedral : 12.625 78.616 3570 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.43 % Favored : 95.53 % Rotamer: Outliers : 2.77 % Allowed : 12.46 % Favored : 84.76 % 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: 0.23 (0.16), residues: 2752 helix: 1.29 (0.14), residues: 1329 sheet: -1.20 (0.31), residues: 308 loop : -0.78 (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 507 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 438 time to evaluate : 2.603 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 outliers start: 69 outliers final: 40 residues processed: 477 average time/residue: 0.3458 time to fit residues: 259.9524 Evaluate side-chains 385 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 345 time to evaluate : 2.763 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2108 time to fit residues: 19.5043 ------------------------------------------------------------------------------- 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: 10.0000 chunk 78 optimal weight: 8.9990 chunk 211 optimal weight: 0.0570 chunk 173 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 overall best weight: 1.0102 ------------------------------------------------------------------------------- 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** ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 134 GLN ** 4 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 63 GLN 7 459 GLN 7 656 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24242 Z= 0.292 Angle : 0.653 11.736 33001 Z= 0.332 Chirality : 0.042 0.156 3724 Planarity : 0.005 0.063 4029 Dihedral : 13.024 69.977 3570 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 2.25 % Allowed : 15.44 % Favored : 82.31 % 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: -0.27 (0.16), residues: 2752 helix: 0.81 (0.14), residues: 1340 sheet: -1.46 (0.33), residues: 264 loop : -0.98 (0.18), residues: 1148 *********************** 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 444 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 388 time to evaluate : 2.600 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 outliers start: 56 outliers final: 26 residues processed: 425 average time/residue: 0.3466 time to fit residues: 234.1734 Evaluate side-chains 353 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 327 time to evaluate : 2.895 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2218 time to fit residues: 14.7126 ------------------------------------------------------------------------------- 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: 0.2980 chunk 191 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 171 optimal weight: 0.0270 chunk 255 optimal weight: 2.9990 chunk 270 optimal weight: 0.0970 chunk 133 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 72 optimal weight: 0.0030 overall best weight: 0.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 145 HIS 7 173 ASN 7 187 HIS 7 366 ASN 7 481 ASN 7 506 GLN 7 545 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.3861 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= 0.177 Angle : 0.601 10.085 33001 Z= 0.303 Chirality : 0.041 0.217 3724 Planarity : 0.004 0.049 4029 Dihedral : 12.987 69.705 3570 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 1.77 % Allowed : 17.33 % Favored : 80.90 % 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: -0.23 (0.16), residues: 2752 helix: 0.85 (0.14), residues: 1337 sheet: -1.40 (0.31), residues: 280 loop : -0.96 (0.18), residues: 1135 *********************** 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 442 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 398 time to evaluate : 2.949 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 outliers start: 44 outliers final: 21 residues processed: 423 average time/residue: 0.3388 time to fit residues: 226.6666 Evaluate side-chains 355 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 334 time to evaluate : 2.789 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2143 time to fit residues: 12.1801 ------------------------------------------------------------------------------- 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: 0.0040 chunk 153 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 201 optimal weight: 8.9990 chunk 111 optimal weight: 0.4980 chunk 230 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 135 HIS 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** ** 3 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 48 HIS 7 187 HIS 7 366 ASN 7 506 GLN 7 545 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24242 Z= 0.215 Angle : 0.607 12.362 33001 Z= 0.305 Chirality : 0.041 0.188 3724 Planarity : 0.004 0.053 4029 Dihedral : 13.100 70.062 3570 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 1.89 % Allowed : 18.78 % Favored : 79.33 % 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: 0.77 (0.14), residues: 1334 sheet: -1.37 (0.32), residues: 266 loop : -1.00 (0.18), residues: 1152 *********************** 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 421 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 374 time to evaluate : 2.561 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 outliers start: 47 outliers final: 18 residues processed: 407 average time/residue: 0.3495 time to fit residues: 223.6843 Evaluate side-chains 349 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 331 time to evaluate : 2.873 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2241 time to fit residues: 11.3775 ------------------------------------------------------------------------------- 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: 0.3980 chunk 243 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 270 optimal weight: 0.2980 chunk 224 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 2 37 HIS ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 99 GLN ** 2 117 ASN ** 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** 6 364 GLN 7 187 HIS 7 366 ASN ** 7 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 621 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24242 Z= 0.197 Angle : 0.609 12.592 33001 Z= 0.303 Chirality : 0.041 0.233 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.097 70.641 3570 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 1.57 % Allowed : 19.98 % Favored : 78.45 % 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: -0.33 (0.16), residues: 2752 helix: 0.79 (0.14), residues: 1338 sheet: -1.32 (0.32), residues: 260 loop : -1.08 (0.18), residues: 1154 *********************** 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 398 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 359 time to evaluate : 2.605 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 outliers start: 39 outliers final: 20 residues processed: 381 average time/residue: 0.3457 time to fit residues: 208.1588 Evaluate side-chains 350 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 330 time to evaluate : 2.617 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2321 time to fit residues: 11.9839 ------------------------------------------------------------------------------- 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: 4.9990 chunk 30 optimal weight: 0.0010 chunk 154 optimal weight: 0.0570 chunk 197 optimal weight: 0.1980 chunk 153 optimal weight: 0.5980 chunk 228 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 overall best weight: 0.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 145 GLN ** 0 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 307 ASN ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 48 HIS ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 545 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24242 Z= 0.179 Angle : 0.607 12.187 33001 Z= 0.301 Chirality : 0.041 0.191 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.079 71.486 3570 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 0.97 % Allowed : 20.87 % Favored : 78.17 % 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: -0.30 (0.16), residues: 2752 helix: 0.83 (0.14), residues: 1340 sheet: -1.25 (0.33), residues: 252 loop : -1.14 (0.18), residues: 1160 *********************** 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: 24 poor density : 362 time to evaluate : 2.788 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: 24 outliers final: 10 residues processed: 374 average time/residue: 0.3484 time to fit residues: 207.5980 Evaluate side-chains 338 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 328 time to evaluate : 2.620 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2133 time to fit residues: 7.6293 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 81 optimal weight: 0.0060 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 171 optimal weight: 0.3980 chunk 183 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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** 0 307 ASN 0 555 GLN 1 398 GLN ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 362 GLN 3 24 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN 4 48 HIS ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN 5 54 GLN ** 6 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24242 Z= 0.255 Angle : 0.666 16.152 33001 Z= 0.329 Chirality : 0.042 0.222 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.242 71.882 3570 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 1.45 % Allowed : 22.32 % Favored : 76.24 % 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: -0.47 (0.16), residues: 2752 helix: 0.68 (0.14), residues: 1353 sheet: -1.46 (0.32), residues: 258 loop : -1.18 (0.18), residues: 1141 *********************** 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 371 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 335 time to evaluate : 2.576 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: 36 outliers final: 21 residues processed: 355 average time/residue: 0.3535 time to fit residues: 198.4158 Evaluate side-chains 338 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 317 time to evaluate : 2.761 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2177 time to fit residues: 12.4845 ------------------------------------------------------------------------------- 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: 0.0170 chunk 258 optimal weight: 1.9990 chunk 235 optimal weight: 0.1980 chunk 251 optimal weight: 0.0980 chunk 151 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 227 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 250 optimal weight: 0.7980 overall best weight: 0.3418 ------------------------------------------------------------------------------- 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** ** 2 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN ** 4 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 377 GLN 7 481 ASN ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24242 Z= 0.188 Angle : 0.641 14.592 33001 Z= 0.316 Chirality : 0.041 0.234 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.131 72.352 3570 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.97 % Rotamer: Outliers : 0.68 % Allowed : 22.56 % Favored : 76.76 % 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: -0.45 (0.16), residues: 2752 helix: 0.69 (0.14), residues: 1352 sheet: -1.30 (0.33), residues: 252 loop : -1.21 (0.18), residues: 1148 *********************** 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 367 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 350 time to evaluate : 2.831 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: 17 outliers final: 10 residues processed: 359 average time/residue: 0.3454 time to fit residues: 199.5197 Evaluate side-chains 334 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 324 time to evaluate : 2.748 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2428 time to fit residues: 8.2447 ------------------------------------------------------------------------------- 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: 0.2980 chunk 265 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 184 optimal weight: 0.0270 chunk 278 optimal weight: 1.9990 chunk 256 optimal weight: 0.6980 chunk 222 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 171 optimal weight: 0.1980 chunk 136 optimal weight: 7.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 20 GLN ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN ** 4 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.5068 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= 0.201 Angle : 0.662 13.967 33001 Z= 0.325 Chirality : 0.041 0.275 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.134 72.762 3570 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.24 % Rotamer: Outliers : 0.24 % Allowed : 23.40 % Favored : 76.36 % 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: -0.46 (0.16), residues: 2752 helix: 0.69 (0.15), residues: 1349 sheet: -1.34 (0.32), residues: 257 loop : -1.20 (0.18), residues: 1146 ********************** 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 342 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 336 time to evaluate : 2.671 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: 6 outliers final: 2 residues processed: 339 average time/residue: 0.3487 time to fit residues: 190.2675 Evaluate side-chains 324 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 2.630 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2287 time to fit residues: 4.4321 ------------------------------------------------------------------------------- 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: 3.9990 chunk 236 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN 0 187 GLN 1 398 GLN 1 463 HIS ** 2 83 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 9 ASN ** 4 46 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 340 ASN ** 6 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.171961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.152202 restraints weight = 43994.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.148512 restraints weight = 56376.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.146580 restraints weight = 50421.553| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 24242 Z= 0.364 Angle : 0.740 13.036 33001 Z= 0.372 Chirality : 0.045 0.248 3724 Planarity : 0.005 0.050 4029 Dihedral : 13.524 72.150 3570 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.78 % Favored : 94.19 % Rotamer: Outliers : 0.68 % Allowed : 22.96 % Favored : 76.36 % 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: -0.83 (0.16), residues: 2752 helix: 0.40 (0.14), residues: 1336 sheet: -1.85 (0.34), residues: 234 loop : -1.32 (0.17), residues: 1182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5181.66 seconds wall clock time: 95 minutes 39.00 seconds (5739.00 seconds total)