Starting phenix.real_space_refine (version: dev) on Thu Dec 15 02:35:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvw_12615/12_2022/7nvw_12615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvw_12615/12_2022/7nvw_12615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvw_12615/12_2022/7nvw_12615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvw_12615/12_2022/7nvw_12615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvw_12615/12_2022/7nvw_12615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvw_12615/12_2022/7nvw_12615_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.935 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "0 PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 673": "OD1" <-> "OD2" Residue "0 PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 23647 Number of models: 1 Model: "" Number of chains: 17 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: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 2 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: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 421 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "T" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 440 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} 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: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1541 SG CYS 0 190 75.340 144.411 46.359 1.00 69.78 S ATOM 943 SG CYS 0 116 73.226 140.912 51.549 1.00 63.31 S ATOM 1083 SG CYS 0 134 69.263 142.212 46.760 1.00 62.63 S ATOM 1252 SG CYS 0 155 71.742 147.057 50.379 1.00 65.39 S ATOM 11119 SG CYS 3 6 21.528 128.473 50.992 1.00 78.91 S ATOM 11143 SG CYS 3 9 19.239 125.716 52.096 1.00 83.27 S ATOM 11315 SG CYS 3 31 21.257 125.412 48.868 1.00 78.66 S ATOM 11336 SG CYS 3 34 18.016 128.180 49.221 1.00 76.83 S ATOM 11280 SG CYS 3 26 21.468 138.116 43.515 1.00 67.16 S ATOM 11423 SG CYS 3 46 18.915 136.141 45.901 1.00 76.84 S ATOM 11445 SG CYS 3 49 20.544 139.337 46.828 1.00 73.51 S ATOM 14188 SG CYS 4 268 125.424 109.723 78.770 1.00 27.11 S ATOM 14207 SG CYS 4 271 128.436 109.399 76.466 1.00 26.62 S ATOM 14292 SG CYS 4 282 128.051 112.519 79.248 1.00 49.53 S ATOM 14312 SG CYS 4 285 125.795 112.326 75.828 1.00 42.84 S ATOM 14080 SG CYS 4 255 136.863 107.356 87.615 1.00 36.25 S ATOM 14097 SG CYS 4 257 136.672 110.832 85.593 1.00 44.83 S ATOM 14246 SG CYS 4 276 135.853 110.519 89.756 1.00 44.04 S ATOM 17300 SG CYS 6 345 131.198 81.512 56.444 1.00 29.82 S ATOM 17322 SG CYS 6 348 130.130 78.460 58.511 1.00 18.10 S ATOM 17479 SG CYS 6 368 127.545 80.464 56.746 1.00 32.98 S ATOM 17500 SG CYS 6 371 129.267 81.894 59.716 1.00 27.07 S ATOM 17420 SG CYS 6 360 132.513 93.203 58.511 1.00 43.10 S ATOM 17438 SG CYS 6 363 135.874 91.607 58.318 1.00 45.55 S ATOM 17587 SG CYS 6 382 133.129 90.690 61.023 1.00 25.70 S ATOM 17604 SG CYS 6 385 135.466 94.540 61.162 1.00 35.79 S ATOM 16864 SG CYS 6 291 122.118 100.777 98.628 1.00 34.40 S ATOM 16886 SG CYS 6 294 118.519 101.048 99.911 1.00 36.86 S ATOM 16975 SG CYS 6 305 119.179 101.531 96.306 1.00 34.09 S ATOM 16998 SG CYS 6 308 119.903 104.032 99.110 1.00 38.36 S Time building chain proxies: 12.90, per 1000 atoms: 0.55 Number of scatterers: 23647 At special positions: 0 Unit cell: (173.25, 170.1, 135.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 146 16.00 P 42 15.00 O 4400 8.00 N 4090 7.00 C 14958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.02 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 01000 " pdb=" FE4 SF4 01000 " - pdb=" SG CYS 0 155 " pdb=" FE1 SF4 01000 " - pdb=" SG CYS 0 190 " 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 6 368 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 371 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 348 " pdb="ZN ZN 6 401 " - pdb=" SG CYS 6 345 " 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 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 16 sheets defined 47.8% alpha, 5.7% beta 21 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain '0' and resid 19 through 34 Processing helix chain '0' and resid 48 through 62 Processing helix chain '0' and resid 77 through 98 removed outlier: 3.801A pdb=" N LYS 0 82 " --> pdb=" O PRO 0 78 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL 0 83 " --> pdb=" O GLU 0 79 " (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 138 Processing helix chain '0' and resid 140 through 148 removed outlier: 3.589A pdb=" N HIS 0 148 " --> pdb=" O ALA 0 144 " (cutoff:3.500A) Processing helix chain '0' and resid 156 through 164 Processing helix chain '0' and resid 177 through 187 removed outlier: 3.668A pdb=" N ALA 0 182 " --> pdb=" O ASP 0 178 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 201 removed outlier: 3.644A pdb=" N ALA 0 195 " --> pdb=" O PRO 0 191 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU 0 200 " --> pdb=" O ARG 0 196 " (cutoff:3.500A) removed outlier: 4.399A 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 215 through 221 removed outlier: 3.782A pdb=" N ASP 0 219 " --> pdb=" O PRO 0 215 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU 0 220 " --> pdb=" O LYS 0 216 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL 0 221 " --> pdb=" O ILE 0 217 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 215 through 221' Processing helix chain '0' and resid 224 through 226 No H-bonds generated for 'chain '0' and resid 224 through 226' Processing helix chain '0' and resid 236 through 245 removed outlier: 3.650A pdb=" N ILE 0 239 " --> pdb=" O ALA 0 236 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASP 0 240 " --> pdb=" O HIS 0 237 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN 0 241 " --> pdb=" O ASN 0 238 " (cutoff:3.500A) Processing helix chain '0' and resid 253 through 276 Processing helix chain '0' and resid 279 through 290 removed outlier: 4.732A pdb=" N GLU 0 284 " --> pdb=" O ARG 0 280 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR 0 285 " --> pdb=" O LEU 0 281 " (cutoff:3.500A) removed outlier: 4.061A 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: 4.377A 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 385 Processing helix chain '0' and resid 395 through 409 removed outlier: 3.716A pdb=" N SER 0 408 " --> pdb=" O ALA 0 404 " (cutoff:3.500A) 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 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 removed outlier: 3.636A pdb=" N GLU 0 586 " --> pdb=" O GLU 0 582 " (cutoff:3.500A) Processing helix chain '0' and resid 603 through 607 Processing helix chain '0' and resid 631 through 642 removed outlier: 3.606A pdb=" N ALA 0 635 " --> pdb=" O ARG 0 631 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU 0 640 " --> pdb=" O ARG 0 636 " (cutoff:3.500A) Processing helix chain '0' and resid 648 through 662 removed outlier: 3.694A pdb=" N HIS 0 659 " --> pdb=" O ASP 0 655 " (cutoff:3.500A) Processing helix chain '0' and resid 682 through 685 Processing helix chain '0' and resid 687 through 692 Processing helix chain '0' and resid 695 through 700 removed outlier: 3.686A 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: 4.405A pdb=" N GLN 1 119 " --> pdb=" O ASN 1 115 " (cutoff:3.500A) Processing helix chain '1' and resid 122 through 133 removed outlier: 3.714A pdb=" N VAL 1 132 " --> pdb=" O TYR 1 128 " (cutoff:3.500A) Processing helix chain '1' and resid 139 through 145 removed outlier: 3.766A pdb=" N TRP 1 143 " --> pdb=" O GLU 1 140 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA 1 144 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN 1 145 " --> pdb=" O PHE 1 142 " (cutoff:3.500A) 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: 3.604A pdb=" N PHE 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE 1 225 " --> pdb=" O TRP 1 221 " (cutoff:3.500A) Processing helix chain '1' and resid 298 through 317 removed outlier: 3.507A pdb=" N ALA 1 302 " --> pdb=" O ASN 1 298 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE 1 303 " --> pdb=" O SER 1 299 " (cutoff:3.500A) removed outlier: 3.968A 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: 3.633A pdb=" N ILE 1 401 " --> pdb=" O SER 1 397 " (cutoff:3.500A) Processing helix chain '1' and resid 410 through 412 No H-bonds generated for 'chain '1' and resid 410 through 412' Processing helix chain '1' and resid 424 through 434 Processing helix chain '1' and resid 456 through 477 removed outlier: 3.736A pdb=" N GLU 1 460 " --> pdb=" O ASP 1 456 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS 1 474 " --> pdb=" O GLU 1 470 " (cutoff:3.500A) Processing helix chain '1' and resid 486 through 514 removed outlier: 4.148A pdb=" N VAL 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS 1 492 " --> pdb=" O GLU 1 488 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE 1 500 " --> pdb=" O ASN 1 496 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU 1 505 " --> pdb=" O GLN 1 501 " (cutoff:3.500A) Proline residue: 1 507 - end of helix Processing helix chain '1' and resid 524 through 546 removed outlier: 3.693A pdb=" N MET 1 528 " --> pdb=" O HIS 1 524 " (cutoff:3.500A) removed outlier: 3.519A 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 removed outlier: 3.677A pdb=" N ARG 2 33 " --> pdb=" O GLY 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 47 removed outlier: 3.909A pdb=" N PHE 2 45 " --> pdb=" O CYS 2 41 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU 2 47 " --> pdb=" O ALA 2 43 " (cutoff:3.500A) Processing helix chain '2' and resid 52 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: 3.561A 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: 3.593A pdb=" N GLN 2 202 " --> pdb=" O SER 2 198 " (cutoff:3.500A) Processing helix chain '2' and resid 208 through 226 removed outlier: 3.664A pdb=" N SER 2 225 " --> pdb=" O GLN 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 230 through 241 removed outlier: 3.654A pdb=" N PHE 2 236 " --> pdb=" O GLU 2 232 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU 2 237 " --> pdb=" O ILE 2 233 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE 2 238 " --> pdb=" O LEU 2 234 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER 2 241 " --> pdb=" O LEU 2 237 " (cutoff:3.500A) 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 331 removed outlier: 4.315A pdb=" N PHE 2 331 " --> pdb=" O LEU 2 327 " (cutoff:3.500A) 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 377 Processing helix chain '2' and resid 385 through 398 removed outlier: 3.616A pdb=" N ARG 2 398 " --> pdb=" O TRP 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 415 through 428 Processing helix chain '2' and resid 445 through 457 removed outlier: 3.815A pdb=" N SER 2 449 " --> pdb=" O PRO 2 445 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP 2 450 " --> 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: 3.949A pdb=" N LEU 3 37 " --> pdb=" O SER 3 33 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 80 removed outlier: 3.764A 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 92 through 110 removed outlier: 4.602A pdb=" N ASN 3 96 " --> pdb=" O LEU 3 92 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE 3 98 " --> pdb=" O GLU 3 94 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU 3 99 " --> pdb=" O TYR 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 115 through 128 removed outlier: 3.744A pdb=" N LYS 3 127 " --> pdb=" O GLU 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 148 removed outlier: 4.120A pdb=" N THR 3 141 " --> pdb=" O LYS 3 137 " (cutoff:3.500A) removed outlier: 3.852A 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: 4.632A pdb=" N MET 4 175 " --> pdb=" O LEU 4 172 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN 4 176 " --> pdb=" O GLN 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 201 through 210 removed outlier: 3.608A pdb=" N ILE 4 209 " --> pdb=" O GLN 4 205 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR 4 210 " --> pdb=" O ALA 4 206 " (cutoff:3.500A) Processing helix chain '4' and resid 220 through 227 removed outlier: 4.824A pdb=" N LEU 4 224 " --> pdb=" O PRO 4 221 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN 4 225 " --> pdb=" O SER 4 222 " (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 Processing helix chain '5' and resid 47 through 63 removed outlier: 4.392A pdb=" N ASN 5 51 " --> pdb=" O GLU 5 48 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL 5 52 " --> pdb=" O LEU 5 49 " (cutoff:3.500A) Processing helix chain '6' and resid 10 through 13 No H-bonds generated for 'chain '6' and resid 10 through 13' Processing helix chain '6' and resid 18 through 20 No H-bonds generated for 'chain '6' and resid 18 through 20' Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 80 through 98 removed outlier: 3.649A pdb=" N TYR 6 90 " --> pdb=" O LYS 6 86 " (cutoff:3.500A) Processing helix chain '6' and resid 124 through 136 removed outlier: 4.316A pdb=" N ASP 6 136 " --> pdb=" O LYS 6 132 " (cutoff:3.500A) Processing helix chain '6' and resid 145 through 157 Processing helix chain '6' and resid 182 through 192 removed outlier: 3.576A pdb=" N LYS 6 187 " --> pdb=" O TYR 6 183 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR 6 188 " --> pdb=" O ASP 6 184 " (cutoff:3.500A) Processing helix chain '6' and resid 206 through 215 Processing helix chain '6' and resid 225 through 236 removed outlier: 3.624A pdb=" N GLU 6 230 " --> pdb=" O SER 6 226 " (cutoff:3.500A) Processing helix chain '6' and resid 315 through 325 removed outlier: 3.887A pdb=" N SER 6 321 " --> pdb=" O HIS 6 317 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR 6 322 " --> pdb=" O LEU 6 318 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N HIS 6 323 " --> pdb=" O ALA 6 319 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N HIS 6 324 " --> pdb=" O ARG 6 320 " (cutoff:3.500A) removed outlier: 4.167A 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 383 through 386 No H-bonds generated for 'chain '6' and resid 383 through 386' Processing helix chain '7' and resid 93 through 103 Processing helix chain '7' and resid 120 through 128 Processing helix chain '7' and resid 133 through 143 removed outlier: 4.395A pdb=" N TYR 7 139 " --> pdb=" O ASP 7 135 " (cutoff:3.500A) Processing helix chain '7' and resid 150 through 161 Processing helix chain '7' and resid 182 through 188 Processing helix chain '7' and resid 192 through 197 Processing helix chain '7' and resid 275 through 286 removed outlier: 4.180A pdb=" N GLU 7 278 " --> pdb=" O GLU 7 275 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS 7 282 " --> pdb=" O GLU 7 279 " (cutoff:3.500A) 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 386 through 388 No H-bonds generated for 'chain '7' and resid 386 through 388' Processing helix chain '7' and resid 410 through 413 No H-bonds generated for 'chain '7' and resid 410 through 413' Processing helix chain '7' and resid 421 through 432 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 449 through 457 removed outlier: 3.726A pdb=" N VAL 7 454 " --> pdb=" O MET 7 450 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU 7 455 " --> pdb=" O PHE 7 451 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR 7 456 " --> pdb=" O ARG 7 452 " (cutoff:3.500A) Processing helix chain '7' and resid 478 through 483 removed outlier: 3.627A 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 Processing helix chain '7' and resid 529 through 534 removed outlier: 4.415A pdb=" N TYR 7 534 " --> pdb=" O ILE 7 531 " (cutoff:3.500A) Processing helix chain '7' and resid 538 through 552 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 613 Processing helix chain '7' and resid 633 through 642 removed outlier: 4.127A pdb=" N ARG 7 642 " --> pdb=" O GLN 7 638 " (cutoff:3.500A) Processing helix chain '7' and resid 668 through 676 Processing helix chain '7' and resid 678 through 683 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 helix chain 'Z' and resid 8 through 10 No H-bonds generated for 'chain 'Z' and resid 8 through 10' Processing sheet with id= A, first strand: chain '0' and resid 478 through 480 removed outlier: 7.665A pdb=" N VAL 0 39 " --> pdb=" O ALA 0 479 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU 0 40 " --> pdb=" O ILE 0 456 " (cutoff:3.500A) removed outlier: 3.678A 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: 4.091A pdb=" N ALA 0 108 " --> pdb=" O TYR 0 175 " (cutoff:3.500A) removed outlier: 6.329A 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 Processing sheet with id= D, first strand: chain '0' and resid 676 through 680 removed outlier: 3.518A pdb=" N VAL 0 536 " --> pdb=" O ALA 0 617 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 307 through 309 removed outlier: 6.233A pdb=" N GLN 2 345 " --> pdb=" O MET 2 334 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N MET 2 334 " --> pdb=" O GLN 2 345 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 431 through 435 removed outlier: 6.793A pdb=" N VAL 2 442 " --> pdb=" O VAL 2 432 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU 2 434 " --> pdb=" O LEU 2 440 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU 2 440 " --> pdb=" O GLU 2 434 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 21 through 23 removed outlier: 3.650A pdb=" N ARG 3 59 " --> pdb=" O VAL 3 23 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '4' and resid 13 through 15 Processing sheet with id= I, first strand: chain '5' and resid 8 through 11 Processing sheet with id= J, first strand: chain '6' and resid 164 through 170 removed outlier: 3.866A pdb=" N ASP 6 66 " --> pdb=" O ILE 6 170 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN 6 103 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL 6 63 " --> pdb=" O GLN 6 103 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY 6 105 " --> pdb=" O VAL 6 63 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL 6 65 " --> pdb=" O GLY 6 105 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE 6 107 " --> pdb=" O VAL 6 65 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL 6 108 " --> pdb=" O LYS 6 116 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS 6 116 " --> pdb=" O VAL 6 108 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LYS 6 110 " --> pdb=" O ALA 6 114 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA 6 114 " --> pdb=" O LYS 6 110 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '7' and resid 83 through 87 removed outlier: 6.144A pdb=" N LYS 7 117 " --> pdb=" O PRO 7 106 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '7' and resid 167 through 171 Processing sheet with id= M, first strand: chain '7' and resid 465 through 467 removed outlier: 3.573A pdb=" N THR 7 467 " --> pdb=" O ILE 7 338 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL 7 339 " --> pdb=" O LEU 7 488 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU 7 490 " --> pdb=" O VAL 7 339 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '7' and resid 362 through 365 removed outlier: 6.362A pdb=" N ALA 7 406 " --> pdb=" O VAL 7 363 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLY 7 365 " --> pdb=" O ALA 7 406 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER 7 408 " --> pdb=" O GLY 7 365 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '7' and resid 657 through 660 removed outlier: 3.898A pdb=" N PHE 7 659 " --> pdb=" O GLN 7 506 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS 7 688 " --> pdb=" O GLU 7 509 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '7' and resid 558 through 561 842 hydrogen bonds defined for protein. 2358 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 7.18 Time building geometry restraints manager: 10.80 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: 10129 1.43 - 1.64: 13855 1.64 - 1.86: 214 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 24210 Sorted by residual: bond pdb=" N MET 3 1 " pdb=" CA MET 3 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.23e+00 bond pdb=" N MET 0 1 " pdb=" CA MET 0 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" C3' DC N 52 " pdb=" O3' DC N 52 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CB CYS 6 385 " pdb=" SG CYS 6 385 " ideal model delta sigma weight residual 1.808 1.777 0.031 3.30e-02 9.18e+02 8.82e-01 bond pdb=" C HIS 2 37 " pdb=" N PRO 2 38 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.30e-02 5.92e+03 7.52e-01 ... (remaining 24205 not shown) Histogram of bond angle deviations from ideal: 73.40 - 85.53: 12 85.53 - 97.65: 0 97.65 - 109.77: 2857 109.77 - 121.89: 25222 121.89 - 134.02: 4824 Bond angle restraints: 32915 Sorted by residual: angle pdb=" C SER 0 462 " pdb=" CA SER 0 462 " pdb=" CB SER 0 462 " ideal model delta sigma weight residual 109.51 114.78 -5.27 1.85e+00 2.92e-01 8.12e+00 angle pdb=" N GLY 0 670 " pdb=" CA GLY 0 670 " pdb=" C GLY 0 670 " ideal model delta sigma weight residual 110.42 114.51 -4.09 1.49e+00 4.50e-01 7.52e+00 angle pdb=" N SER 0 462 " pdb=" CA SER 0 462 " pdb=" C SER 0 462 " ideal model delta sigma weight residual 110.20 106.50 3.70 1.44e+00 4.82e-01 6.60e+00 angle pdb=" C VAL 0 242 " pdb=" CA VAL 0 242 " pdb=" CB VAL 0 242 " ideal model delta sigma weight residual 112.22 109.14 3.08 1.38e+00 5.25e-01 4.99e+00 angle pdb=" N HIS 0 210 " pdb=" CA HIS 0 210 " pdb=" C HIS 0 210 " ideal model delta sigma weight residual 113.01 110.51 2.50 1.20e+00 6.94e-01 4.32e+00 ... (remaining 32910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 14139 34.97 - 69.93: 381 69.93 - 104.90: 26 104.90 - 139.86: 0 139.86 - 174.83: 1 Dihedral angle restraints: 14547 sinusoidal: 6203 harmonic: 8344 Sorted by residual: 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 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+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 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" C4' DC N 52 " pdb=" C3' DC N 52 " pdb=" O3' DC N 52 " pdb=" P DT N 53 " ideal model delta sinusoidal sigma weight residual 220.00 45.17 174.83 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 14544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2621 0.028 - 0.056: 645 0.056 - 0.084: 235 0.084 - 0.112: 171 0.112 - 0.140: 39 Chirality restraints: 3711 Sorted by residual: chirality pdb=" CA ILE 6 199 " pdb=" N ILE 6 199 " pdb=" C ILE 6 199 " pdb=" CB ILE 6 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 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 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE 7 407 " pdb=" N ILE 7 407 " pdb=" C ILE 7 407 " pdb=" CB ILE 7 407 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 3708 not shown) Planarity restraints: 4050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER 0 462 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO 0 463 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO 0 463 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO 0 463 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 1 211 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO 1 212 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO 1 212 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO 1 212 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY 7 582 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO 7 583 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO 7 583 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO 7 583 " -0.017 5.00e-02 4.00e+02 ... (remaining 4047 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 246 2.56 - 3.14: 20414 3.14 - 3.73: 38058 3.73 - 4.31: 50788 4.31 - 4.90: 83348 Nonbonded interactions: 192854 Sorted by model distance: nonbonded pdb=" OG SER 7 394 " pdb=" OP2 DG T -41 " model vdw 1.971 2.440 nonbonded pdb=" O SER 1 195 " pdb=" OG1 THR 1 199 " model vdw 2.000 2.440 nonbonded pdb=" OG1 THR 0 571 " pdb=" OD1 ASP 0 573 " model vdw 2.009 2.440 nonbonded pdb=" OG SER 4 62 " pdb=" O LEU 4 132 " model vdw 2.023 2.440 nonbonded pdb=" OG SER 0 44 " pdb=" O THR 0 46 " model vdw 2.034 2.440 ... (remaining 192849 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 42 5.49 5 S 146 5.16 5 C 14958 2.51 5 N 4090 2.21 5 O 4400 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.580 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: 21.860 Check model and map are aligned: 0.320 Convert atoms to be neutral: 0.190 Process input model: 71.870 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 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 : 0.002 0.038 24210 Z= 0.143 Angle : 0.452 5.270 32915 Z= 0.264 Chirality : 0.036 0.140 3711 Planarity : 0.002 0.059 4050 Dihedral : 15.455 174.826 9125 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2768 helix: 2.02 (0.15), residues: 1307 sheet: -1.53 (0.31), residues: 307 loop : -0.60 (0.18), residues: 1154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 853 time to evaluate : 2.718 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 853 average time/residue: 0.3857 time to fit residues: 490.3291 Evaluate side-chains 465 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 2.950 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 256 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 262 ASN ** 0 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 181 GLN 2 264 HIS 2 289 ASN ** 3 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 HIS 4 148 ASN ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 187 GLN 4 235 GLN 6 147 ASN 6 235 HIS ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 349 GLN ** 6 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 373 GLN ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 24210 Z= 0.264 Angle : 0.637 10.089 32915 Z= 0.327 Chirality : 0.042 0.243 3711 Planarity : 0.004 0.055 4050 Dihedral : 11.416 173.008 3503 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 95.99 % Rotamer Outliers : 0.24 % 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: 0.25 (0.16), residues: 2768 helix: 1.36 (0.14), residues: 1337 sheet: -1.59 (0.29), residues: 323 loop : -0.68 (0.19), residues: 1108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 581 time to evaluate : 3.107 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0 residues processed: 586 average time/residue: 0.3637 time to fit residues: 328.1000 Evaluate side-chains 410 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 2.879 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 256 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 0 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 237 HIS ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 662 GLN 0 723 GLN 1 474 HIS ** 2 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 366 HIS 2 390 GLN 3 57 ASN ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 HIS 4 173 GLN ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 187 GLN 6 265 GLN ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 355 GLN ** 6 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 629 HIS 7 709 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 24210 Z= 0.351 Angle : 0.707 9.607 32915 Z= 0.363 Chirality : 0.044 0.182 3711 Planarity : 0.005 0.063 4050 Dihedral : 11.759 173.777 3503 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.24 % 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: -0.54 (0.16), residues: 2768 helix: 0.63 (0.14), residues: 1339 sheet: -2.06 (0.28), residues: 298 loop : -0.96 (0.18), residues: 1131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 504 time to evaluate : 2.598 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 outliers start: 6 outliers final: 2 residues processed: 507 average time/residue: 0.3592 time to fit residues: 283.3427 Evaluate side-chains 373 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 371 time to evaluate : 2.846 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2274 time to fit residues: 4.7088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 133 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 272 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 73 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN 0 145 GLN 0 148 HIS ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 384 HIS ** 2 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 GLN 2 345 GLN ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 HIS ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN 6 265 GLN ** 6 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 187 HIS ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 497 GLN ** 7 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 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 : 0.004 0.045 24210 Z= 0.226 Angle : 0.621 9.749 32915 Z= 0.318 Chirality : 0.042 0.249 3711 Planarity : 0.004 0.076 4050 Dihedral : 11.742 172.681 3503 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.08 % Favored : 95.88 % Rotamer Outliers : 0.08 % 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: -0.34 (0.16), residues: 2768 helix: 0.78 (0.14), residues: 1346 sheet: -1.76 (0.29), residues: 298 loop : -0.93 (0.18), residues: 1124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 488 time to evaluate : 2.626 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: 2 outliers final: 0 residues processed: 489 average time/residue: 0.3436 time to fit residues: 265.4866 Evaluate side-chains 367 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 2.748 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 148 HIS ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 18 ASN ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 65 GLN ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 677 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 24210 Z= 0.281 Angle : 0.653 10.011 32915 Z= 0.335 Chirality : 0.043 0.204 3711 Planarity : 0.005 0.071 4050 Dihedral : 11.819 173.931 3503 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.09 % Rotamer Outliers : 0.08 % 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: -0.52 (0.16), residues: 2768 helix: 0.61 (0.14), residues: 1345 sheet: -1.90 (0.28), residues: 308 loop : -0.95 (0.18), residues: 1115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 474 time to evaluate : 2.903 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: 2 outliers final: 2 residues processed: 475 average time/residue: 0.3495 time to fit residues: 262.5584 Evaluate side-chains 350 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 348 time to evaluate : 2.775 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2251 time to fit residues: 4.6082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 0.9980 chunk 245 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 272 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 24210 Z= 0.221 Angle : 0.625 9.687 32915 Z= 0.316 Chirality : 0.042 0.283 3711 Planarity : 0.004 0.062 4050 Dihedral : 11.823 173.895 3503 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.30 % Favored : 95.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2768 helix: 0.71 (0.14), residues: 1352 sheet: -1.89 (0.29), residues: 286 loop : -1.05 (0.18), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 2.745 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: 0 outliers final: 0 residues processed: 474 average time/residue: 0.3332 time to fit residues: 251.4596 Evaluate side-chains 353 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 199 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 229 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 165 optimal weight: 0.0770 chunk 125 optimal weight: 0.3980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 328 HIS 0 368 GLN 0 519 ASN ** 0 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 263 GLN 2 264 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 145 HIS ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 190 GLN 7 377 GLN ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 591 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 24210 Z= 0.206 Angle : 0.623 11.761 32915 Z= 0.314 Chirality : 0.042 0.310 3711 Planarity : 0.004 0.056 4050 Dihedral : 11.824 174.415 3503 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % Rotamer Outliers : 0.04 % 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: -0.42 (0.16), residues: 2768 helix: 0.74 (0.14), residues: 1350 sheet: -1.58 (0.31), residues: 267 loop : -1.11 (0.18), residues: 1151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 465 time to evaluate : 2.669 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 outliers start: 1 outliers final: 1 residues processed: 466 average time/residue: 0.3304 time to fit residues: 247.3702 Evaluate side-chains 346 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 345 time to evaluate : 2.763 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2649 time to fit residues: 4.2994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 363 GLN ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 227 HIS ** 6 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 377 GLN ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 24210 Z= 0.228 Angle : 0.637 9.261 32915 Z= 0.323 Chirality : 0.043 0.256 3711 Planarity : 0.004 0.053 4050 Dihedral : 11.855 175.111 3503 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.38 % Rotamer Outliers : 0.04 % 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: -0.48 (0.16), residues: 2768 helix: 0.65 (0.14), residues: 1357 sheet: -1.60 (0.31), residues: 264 loop : -1.11 (0.18), residues: 1147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 453 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 outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.3347 time to fit residues: 244.5427 Evaluate side-chains 337 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 2.825 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 253 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 228 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 252 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 264 HIS 3 57 ASN ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 240 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 377 GLN ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 591 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 24210 Z= 0.256 Angle : 0.673 14.051 32915 Z= 0.344 Chirality : 0.043 0.243 3711 Planarity : 0.004 0.055 4050 Dihedral : 11.911 175.597 3503 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2768 helix: 0.53 (0.14), residues: 1346 sheet: -1.64 (0.31), residues: 274 loop : -1.12 (0.18), residues: 1148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.3325 time to fit residues: 233.9070 Evaluate side-chains 335 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 2.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 0.6980 chunk 267 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 280 optimal weight: 0.0470 chunk 258 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 137 optimal weight: 0.0670 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 240 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 377 GLN ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 24210 Z= 0.206 Angle : 0.656 15.077 32915 Z= 0.332 Chirality : 0.043 0.257 3711 Planarity : 0.004 0.066 4050 Dihedral : 11.910 175.401 3503 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2768 helix: 0.62 (0.14), residues: 1348 sheet: -1.52 (0.31), residues: 272 loop : -1.10 (0.18), residues: 1148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 2.796 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 outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.3370 time to fit residues: 238.8710 Evaluate side-chains 346 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.590 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 0.5980 chunk 238 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 0 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 496 ASN ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 237 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 377 GLN ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 576 ASN 7 591 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.142391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.125033 restraints weight = 57310.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.124540 restraints weight = 92412.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.125014 restraints weight = 88967.189| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 24210 Z= 0.274 Angle : 0.681 15.935 32915 Z= 0.347 Chirality : 0.043 0.225 3711 Planarity : 0.005 0.058 4050 Dihedral : 11.991 176.520 3503 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.60 % Favored : 94.36 % Rotamer Outliers : 0.04 % 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: -0.62 (0.16), residues: 2768 helix: 0.53 (0.14), residues: 1346 sheet: -1.67 (0.29), residues: 294 loop : -1.11 (0.18), residues: 1128 =============================================================================== Job complete usr+sys time: 5377.01 seconds wall clock time: 98 minutes 46.35 seconds (5926.35 seconds total)