Starting phenix.real_space_refine on Wed Dec 13 03:49:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/12_2023/7nvx_12616_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/12_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_12616/12_2023/7nvx_12616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/12_2023/7nvx_12616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/12_2023/7nvx_12616_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvx_12616/12_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 12.14, 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: 10.66 Conformation dependent library (CDL) restraints added in 4.0 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: 10.64 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: 7.66 Time building geometry restraints manager: 11.23 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: 13469 24.09 - 48.18: 941 48.18 - 72.27: 135 72.27 - 96.36: 18 96.36 - 120.45: 1 Dihedral angle restraints: 14564 sinusoidal: 6279 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 14561 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: 14.910 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: 0.000 Extract box with map and model: 15.820 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 75.520 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.220 ------------------------------------------------------------------------------- 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 : 15.663 120.451 9180 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 2 96 HIS 0.013 0.001 HIS 4 258 PHE 0.007 0.001 PHE 4 50 TYR 0.015 0.001 TYR 7 581 ARG 0.006 0.000 ARG 7 62 *********************** 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 : 2.836 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: 0.3792 time to fit residues: 392.3244 Evaluate side-chains 408 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 2.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4839 ------------------------------------------------------------------------------- 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 ** 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: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24242 Z= 0.267 Angle : 0.664 11.283 33001 Z= 0.342 Chirality : 0.043 0.239 3724 Planarity : 0.005 0.093 4029 Dihedral : 12.680 78.646 3602 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 2.65 % Allowed : 12.59 % 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: 0.24 (0.16), residues: 2752 helix: 1.30 (0.14), residues: 1329 sheet: -1.20 (0.31), residues: 308 loop : -0.78 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP 2 96 HIS 0.013 0.002 HIS 2 424 PHE 0.031 0.002 PHE 0 332 TYR 0.024 0.002 TYR 0 410 ARG 0.009 0.001 ARG 7 62 *********************** 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 505 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 439 time to evaluate : 2.616 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: 66 outliers final: 38 residues processed: 475 average time/residue: 0.3497 time to fit residues: 263.2510 Evaluate side-chains 384 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 346 time to evaluate : 2.601 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2080 time to fit residues: 18.6174 ------------------------------------------------------------------------------- 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: 2.9990 chunk 78 optimal weight: 6.9990 chunk 211 optimal weight: 0.0050 chunk 173 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 254 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 204 optimal weight: 9.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- 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 2 362 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** 4 205 GLN 5 63 GLN 7 459 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24242 Z= 0.320 Angle : 0.669 11.750 33001 Z= 0.341 Chirality : 0.043 0.165 3724 Planarity : 0.005 0.064 4029 Dihedral : 13.116 69.638 3602 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 2.25 % Allowed : 15.88 % Favored : 81.87 % 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: 0.79 (0.14), residues: 1339 sheet: -1.53 (0.33), residues: 264 loop : -0.98 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP 2 96 HIS 0.011 0.002 HIS 1 384 PHE 0.024 0.002 PHE 4 50 TYR 0.022 0.002 TYR 4 71 ARG 0.011 0.001 ARG 7 62 *********************** 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 436 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 380 time to evaluate : 2.489 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: 28 residues processed: 417 average time/residue: 0.3467 time to fit residues: 229.1149 Evaluate side-chains 347 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 319 time to evaluate : 2.739 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2244 time to fit residues: 15.1236 ------------------------------------------------------------------------------- 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: 0.5980 chunk 132 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 270 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 242 optimal weight: 0.0000 chunk 72 optimal weight: 0.3980 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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** 0 555 GLN 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** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 145 HIS 5 54 GLN 7 173 ASN 7 187 HIS 7 481 ASN 7 656 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.3864 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= 0.200 Angle : 0.614 9.983 33001 Z= 0.309 Chirality : 0.041 0.205 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.121 69.430 3602 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.86 % Rotamer: Outliers : 1.73 % Allowed : 17.81 % Favored : 80.46 % 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: -0.31 (0.16), residues: 2752 helix: 0.80 (0.14), residues: 1332 sheet: -1.52 (0.32), residues: 269 loop : -1.00 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 2 96 HIS 0.014 0.002 HIS 7 187 PHE 0.039 0.002 PHE 2 261 TYR 0.032 0.002 TYR 3 95 ARG 0.009 0.000 ARG 7 62 *********************** 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 432 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 389 time to evaluate : 2.739 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: 43 outliers final: 23 residues processed: 420 average time/residue: 0.3513 time to fit residues: 233.3286 Evaluate side-chains 354 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 331 time to evaluate : 2.614 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2120 time to fit residues: 12.6907 ------------------------------------------------------------------------------- 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: 0.0770 chunk 153 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 230 optimal weight: 0.0030 chunk 187 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 242 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 overall best weight: 0.9352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 135 HIS ** 0 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 398 GLN 2 37 HIS ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 224 GLN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 187 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24242 Z= 0.273 Angle : 0.634 11.090 33001 Z= 0.320 Chirality : 0.042 0.183 3724 Planarity : 0.004 0.051 4029 Dihedral : 13.315 69.490 3602 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 2.37 % Allowed : 19.06 % Favored : 78.57 % 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: -0.46 (0.16), residues: 2752 helix: 0.65 (0.14), residues: 1334 sheet: -1.60 (0.32), residues: 281 loop : -1.04 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP 0 552 HIS 0.014 0.002 HIS 7 187 PHE 0.036 0.002 PHE 2 261 TYR 0.028 0.002 TYR 0 674 ARG 0.010 0.001 ARG 7 62 *********************** 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 413 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 354 time to evaluate : 2.538 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: 59 outliers final: 25 residues processed: 390 average time/residue: 0.3542 time to fit residues: 216.2014 Evaluate side-chains 338 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 313 time to evaluate : 2.600 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2199 time to fit residues: 13.8299 ------------------------------------------------------------------------------- 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: 10.0000 chunk 243 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 270 optimal weight: 0.0980 chunk 224 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 0 560 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** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 187 HIS 7 621 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24242 Z= 0.225 Angle : 0.624 13.235 33001 Z= 0.311 Chirality : 0.041 0.223 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.300 69.916 3602 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 1.69 % Allowed : 20.87 % Favored : 77.44 % 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: 0.67 (0.14), residues: 1331 sheet: -1.62 (0.32), residues: 276 loop : -1.06 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP 0 552 HIS 0.015 0.001 HIS 7 187 PHE 0.022 0.002 PHE 4 50 TYR 0.026 0.001 TYR 0 674 ARG 0.010 0.000 ARG 7 62 *********************** 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 381 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 339 time to evaluate : 2.650 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: 42 outliers final: 18 residues processed: 370 average time/residue: 0.3540 time to fit residues: 208.2611 Evaluate side-chains 328 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 310 time to evaluate : 2.797 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2221 time to fit residues: 11.3893 ------------------------------------------------------------------------------- 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: 0.0770 chunk 30 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 228 optimal weight: 0.0060 chunk 151 optimal weight: 0.0970 chunk 269 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.2752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 145 GLN ** 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 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 117 ASN ** 4 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24242 Z= 0.179 Angle : 0.608 11.753 33001 Z= 0.304 Chirality : 0.040 0.219 3724 Planarity : 0.004 0.058 4029 Dihedral : 13.191 71.125 3602 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 1.37 % Allowed : 21.39 % Favored : 77.24 % 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: -0.44 (0.16), residues: 2752 helix: 0.67 (0.14), residues: 1349 sheet: -1.45 (0.32), residues: 270 loop : -1.10 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP 0 552 HIS 0.008 0.001 HIS 3 28 PHE 0.030 0.001 PHE 2 261 TYR 0.044 0.001 TYR 3 125 ARG 0.008 0.000 ARG 7 62 *********************** 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 393 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 359 time to evaluate : 2.587 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: 34 outliers final: 16 residues processed: 382 average time/residue: 0.3473 time to fit residues: 209.5243 Evaluate side-chains 344 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 328 time to evaluate : 2.585 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2388 time to fit residues: 10.4574 ------------------------------------------------------------------------------- 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: 0.5980 chunk 107 optimal weight: 4.9990 chunk 161 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 171 optimal weight: 0.0060 chunk 183 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.7376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 187 GLN 0 723 GLN 2 20 GLN ** 2 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN 5 54 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: 0.6618 moved from start: 0.4750 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= 0.245 Angle : 0.652 11.773 33001 Z= 0.324 Chirality : 0.042 0.238 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.286 71.554 3602 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 0.92 % Allowed : 22.48 % Favored : 76.60 % 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: 0.63 (0.14), residues: 1349 sheet: -1.56 (0.32), residues: 275 loop : -1.16 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP 0 552 HIS 0.007 0.001 HIS 3 28 PHE 0.026 0.002 PHE 2 261 TYR 0.043 0.002 TYR 3 125 ARG 0.009 0.000 ARG 7 62 *********************** 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: 23 poor density : 341 time to evaluate : 3.024 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: 23 outliers final: 7 residues processed: 357 average time/residue: 0.3682 time to fit residues: 206.4009 Evaluate side-chains 328 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 321 time to evaluate : 2.639 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2209 time to fit residues: 6.8117 ------------------------------------------------------------------------------- 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: 0.7980 chunk 258 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 251 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 227 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 250 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** 2 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 24 ASN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 GLN ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 537 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24242 Z= 0.238 Angle : 0.664 14.728 33001 Z= 0.330 Chirality : 0.042 0.256 3724 Planarity : 0.004 0.088 4029 Dihedral : 13.329 71.890 3602 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 0.52 % Allowed : 23.44 % Favored : 76.04 % 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: 0.60 (0.14), residues: 1342 sheet: -1.64 (0.31), residues: 275 loop : -1.23 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP 0 552 HIS 0.007 0.001 HIS 3 28 PHE 0.043 0.002 PHE 6 331 TYR 0.040 0.002 TYR 3 125 ARG 0.013 0.000 ARG 2 58 *********************** 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 340 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 327 time to evaluate : 2.748 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 outliers start: 13 outliers final: 11 residues processed: 329 average time/residue: 0.3675 time to fit residues: 189.8822 Evaluate side-chains 325 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 314 time to evaluate : 2.864 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2427 time to fit residues: 8.6760 ------------------------------------------------------------------------------- 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: 0.9980 chunk 265 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 126 optimal weight: 0.0770 chunk 184 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 222 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 171 optimal weight: 0.0570 chunk 136 optimal weight: 6.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- 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** ** 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 ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24242 Z= 0.211 Angle : 0.660 14.463 33001 Z= 0.327 Chirality : 0.042 0.262 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.295 72.436 3602 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 0.24 % Allowed : 23.44 % Favored : 76.32 % 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: -0.63 (0.16), residues: 2752 helix: 0.60 (0.14), residues: 1346 sheet: -1.63 (0.32), residues: 271 loop : -1.28 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP 0 552 HIS 0.007 0.001 HIS 3 28 PHE 0.046 0.002 PHE 2 261 TYR 0.040 0.002 TYR 3 125 ARG 0.009 0.000 ARG 7 62 ********************** 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 339 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 333 time to evaluate : 2.736 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 outliers start: 6 outliers final: 2 residues processed: 337 average time/residue: 0.3637 time to fit residues: 194.3301 Evaluate side-chains 315 residues out of total 2487 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 313 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2329 time to fit residues: 4.4398 ------------------------------------------------------------------------------- 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: 4.9990 chunk 236 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 222 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 228 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 307 ASN ** 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** ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 340 ASN 7 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.173733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.154262 restraints weight = 44468.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150429 restraints weight = 57964.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.148017 restraints weight = 49704.942| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 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 : 0.004 0.044 24242 Z= 0.259 Angle : 0.692 14.289 33001 Z= 0.341 Chirality : 0.043 0.261 3724 Planarity : 0.004 0.049 4029 Dihedral : 13.450 72.588 3602 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 0.32 % Allowed : 23.60 % Favored : 76.08 % 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: -0.74 (0.16), residues: 2752 helix: 0.52 (0.14), residues: 1350 sheet: -1.73 (0.31), residues: 288 loop : -1.34 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP 0 552 HIS 0.008 0.001 HIS 2 373 PHE 0.021 0.002 PHE 7 659 TYR 0.036 0.002 TYR 3 125 ARG 0.012 0.000 ARG 7 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5210.55 seconds wall clock time: 96 minutes 9.01 seconds (5769.01 seconds total)