Starting phenix.real_space_refine on Tue Mar 19 08:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvw_12615/03_2024/7nvw_12615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvw_12615/03_2024/7nvw_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_12615/03_2024/7nvw_12615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvw_12615/03_2024/7nvw_12615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvw_12615/03_2024/7nvw_12615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvw_12615/03_2024/7nvw_12615_updated.pdb" } resolution = 4.3 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= -0.005 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.81, per 1000 atoms: 0.54 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: 9.75 Conformation dependent library (CDL) restraints added in 3.7 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: 9.10 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: 7.09 Time building geometry restraints manager: 10.56 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: 14169 34.97 - 69.93: 387 69.93 - 104.90: 26 104.90 - 139.86: 0 139.86 - 174.83: 1 Dihedral angle restraints: 14583 sinusoidal: 6239 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 14580 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 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: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.130 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 74.170 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 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 : 15.515 174.826 9161 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 96 HIS 0.007 0.001 HIS 4 258 PHE 0.011 0.001 PHE 4 69 TYR 0.010 0.001 TYR 7 534 ARG 0.004 0.000 ARG 2 58 *********************** 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 : 2.740 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 REVERT: 0 438 MET cc_start: 0.7073 (ptp) cc_final: 0.4957 (ptp) REVERT: 0 439 ASP cc_start: 0.7387 (p0) cc_final: 0.6750 (t0) REVERT: 0 466 ILE cc_start: 0.7567 (mt) cc_final: 0.7299 (mm) REVERT: 0 545 MET cc_start: 0.8190 (ttp) cc_final: 0.7778 (ttm) REVERT: 0 719 TYR cc_start: 0.7466 (t80) cc_final: 0.7028 (t80) REVERT: 1 500 PHE cc_start: 0.6217 (m-80) cc_final: 0.5964 (m-10) REVERT: 2 73 LEU cc_start: 0.8043 (pp) cc_final: 0.7526 (tt) REVERT: 2 313 TYR cc_start: 0.8229 (m-80) cc_final: 0.7857 (m-80) REVERT: 2 373 HIS cc_start: 0.7793 (t-90) cc_final: 0.7207 (t-90) REVERT: 2 408 LEU cc_start: 0.7104 (tp) cc_final: 0.6838 (tp) REVERT: 2 448 HIS cc_start: 0.7124 (t-90) cc_final: 0.6593 (t-90) REVERT: 3 74 ILE cc_start: 0.8226 (mt) cc_final: 0.8006 (mt) REVERT: 3 99 LEU cc_start: 0.8069 (mp) cc_final: 0.7718 (mp) REVERT: 4 224 LEU cc_start: 0.9009 (tp) cc_final: 0.8530 (tp) REVERT: 5 22 TYR cc_start: 0.7247 (t80) cc_final: 0.6955 (t80) REVERT: 5 44 PHE cc_start: 0.6521 (t80) cc_final: 0.6224 (t80) REVERT: 5 62 ASP cc_start: 0.7751 (m-30) cc_final: 0.7467 (m-30) REVERT: 6 79 ASN cc_start: 0.7612 (t0) cc_final: 0.7267 (t0) REVERT: 6 104 ILE cc_start: 0.8956 (tt) cc_final: 0.8672 (tt) REVERT: 6 171 PHE cc_start: 0.8301 (t80) cc_final: 0.8038 (t80) REVERT: 6 184 ASP cc_start: 0.4073 (t0) cc_final: 0.3047 (t0) REVERT: 7 86 LEU cc_start: 0.7726 (tp) cc_final: 0.7399 (tt) REVERT: 7 289 TYR cc_start: 0.4748 (m-80) cc_final: 0.4469 (m-80) REVERT: 7 473 GLU cc_start: 0.6541 (mp0) cc_final: 0.6113 (mm-30) REVERT: 7 483 LEU cc_start: 0.8670 (mt) cc_final: 0.8350 (tt) REVERT: 7 525 ILE cc_start: 0.8601 (pt) cc_final: 0.8249 (pt) REVERT: W 284 SER cc_start: 0.8689 (t) cc_final: 0.8379 (p) outliers start: 0 outliers final: 0 residues processed: 853 average time/residue: 0.3974 time to fit residues: 500.7452 Evaluate side-chains 469 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 2.743 ------------------------------------------------------------------------------- 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: 0.0870 chunk 85 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 256 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 2 362 GLN 2 390 GLN ** 3 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 HIS 4 148 ASN 4 179 ASN 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 7 373 GLN ** 7 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24210 Z= 0.224 Angle : 0.614 9.771 32915 Z= 0.315 Chirality : 0.042 0.250 3711 Planarity : 0.004 0.051 4050 Dihedral : 11.617 172.828 3539 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 0.16 % Allowed : 5.91 % Favored : 93.93 % 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: 0.35 (0.16), residues: 2768 helix: 1.46 (0.14), residues: 1335 sheet: -1.61 (0.29), residues: 323 loop : -0.63 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 1 476 HIS 0.009 0.001 HIS 4 258 PHE 0.030 0.002 PHE 4 50 TYR 0.038 0.002 TYR 3 125 ARG 0.013 0.001 ARG 2 226 *********************** 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 600 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 596 time to evaluate : 2.766 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: 0 264 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6817 (mt-10) REVERT: 0 370 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8393 (mmtt) REVERT: 0 545 MET cc_start: 0.8011 (ttp) cc_final: 0.7723 (ttm) REVERT: 0 596 LEU cc_start: 0.9276 (tp) cc_final: 0.8910 (tt) REVERT: 0 719 TYR cc_start: 0.7411 (t80) cc_final: 0.7202 (t80) REVERT: 1 309 HIS cc_start: 0.6001 (m-70) cc_final: 0.5660 (m90) REVERT: 1 503 THR cc_start: 0.8086 (p) cc_final: 0.7841 (p) REVERT: 2 73 LEU cc_start: 0.8075 (pp) cc_final: 0.7788 (tt) REVERT: 2 98 THR cc_start: 0.5776 (t) cc_final: 0.5512 (m) REVERT: 2 313 TYR cc_start: 0.8275 (m-80) cc_final: 0.7767 (m-80) REVERT: 2 323 LEU cc_start: 0.8843 (tp) cc_final: 0.8580 (tp) REVERT: 2 365 ILE cc_start: 0.8600 (pt) cc_final: 0.8270 (tp) REVERT: 2 373 HIS cc_start: 0.7768 (t-90) cc_final: 0.7448 (t-90) REVERT: 2 395 GLU cc_start: 0.7926 (pt0) cc_final: 0.7714 (tt0) REVERT: 2 408 LEU cc_start: 0.7072 (tp) cc_final: 0.6744 (tp) REVERT: 2 435 ASN cc_start: 0.6291 (t0) cc_final: 0.5684 (t0) REVERT: 2 448 HIS cc_start: 0.6804 (t-90) cc_final: 0.6360 (t-170) REVERT: 5 22 TYR cc_start: 0.7235 (t80) cc_final: 0.6595 (t80) REVERT: 5 44 PHE cc_start: 0.6127 (t80) cc_final: 0.5493 (t80) REVERT: 5 51 ASN cc_start: 0.6833 (p0) cc_final: 0.6312 (t0) REVERT: 6 79 ASN cc_start: 0.7471 (t0) cc_final: 0.7244 (t0) REVERT: 6 104 ILE cc_start: 0.8833 (tt) cc_final: 0.8537 (tt) REVERT: 6 137 MET cc_start: 0.6421 (tpp) cc_final: 0.5647 (tpt) REVERT: 7 483 LEU cc_start: 0.8762 (mt) cc_final: 0.8361 (tt) REVERT: 7 494 MET cc_start: 0.6539 (mmp) cc_final: 0.5877 (mmt) REVERT: 7 505 VAL cc_start: 0.8790 (t) cc_final: 0.8401 (t) REVERT: 7 661 SER cc_start: 0.8314 (t) cc_final: 0.8106 (t) outliers start: 4 outliers final: 0 residues processed: 599 average time/residue: 0.3575 time to fit residues: 330.3823 Evaluate side-chains 424 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 424 time to evaluate : 2.847 ------------------------------------------------------------------------------- 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: 3.9990 chunk 79 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 277 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 1 474 HIS ** 2 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 GLN ** 2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 366 HIS 3 57 ASN ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 HIS 4 65 GLN 4 173 GLN 4 179 ASN 4 187 GLN 6 257 HIS 6 265 GLN ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 355 GLN ** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 24210 Z= 0.470 Angle : 0.795 11.931 32915 Z= 0.410 Chirality : 0.046 0.173 3711 Planarity : 0.006 0.064 4050 Dihedral : 12.088 174.469 3539 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 0.32 % Allowed : 7.43 % Favored : 92.25 % 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: -0.84 (0.15), residues: 2768 helix: 0.36 (0.13), residues: 1335 sheet: -2.15 (0.28), residues: 304 loop : -1.10 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP 1 221 HIS 0.013 0.002 HIS 0 328 PHE 0.038 0.003 PHE 2 45 TYR 0.044 0.003 TYR 3 125 ARG 0.014 0.001 ARG 2 58 *********************** 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 498 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 490 time to evaluate : 2.696 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: 0 1 MET cc_start: 0.3704 (mmt) cc_final: 0.3251 (tpt) REVERT: 0 264 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6929 (mt-10) REVERT: 0 345 ARG cc_start: 0.7008 (ptp-110) cc_final: 0.5678 (ttm110) REVERT: 0 438 MET cc_start: 0.6883 (ptp) cc_final: 0.6656 (ptp) REVERT: 0 490 LEU cc_start: 0.8784 (pp) cc_final: 0.8522 (pp) REVERT: 0 596 LEU cc_start: 0.9317 (tp) cc_final: 0.9062 (tt) REVERT: 1 117 MET cc_start: 0.5470 (ppp) cc_final: 0.4048 (tpt) REVERT: 1 320 ARG cc_start: 0.4657 (ppt170) cc_final: 0.4304 (ttp-170) REVERT: 1 461 LEU cc_start: 0.8141 (mt) cc_final: 0.7747 (mt) REVERT: 1 499 ARG cc_start: 0.5951 (mtt180) cc_final: 0.5566 (mtt180) REVERT: 2 58 ARG cc_start: 0.7166 (mtp180) cc_final: 0.6886 (mtp-110) REVERT: 2 73 LEU cc_start: 0.8266 (pp) cc_final: 0.7965 (tt) REVERT: 2 98 THR cc_start: 0.5761 (t) cc_final: 0.5378 (m) REVERT: 2 174 ASP cc_start: 0.7230 (p0) cc_final: 0.7015 (p0) REVERT: 2 365 ILE cc_start: 0.8736 (pt) cc_final: 0.8334 (tp) REVERT: 2 373 HIS cc_start: 0.8228 (t-90) cc_final: 0.7530 (t-90) REVERT: 2 408 LEU cc_start: 0.7452 (tp) cc_final: 0.6986 (tp) REVERT: 2 448 HIS cc_start: 0.6830 (t-90) cc_final: 0.6431 (t-170) REVERT: 3 99 LEU cc_start: 0.8052 (mp) cc_final: 0.7527 (mp) REVERT: 3 106 VAL cc_start: 0.9023 (t) cc_final: 0.8427 (t) REVERT: 5 34 ILE cc_start: 0.6954 (mt) cc_final: 0.6679 (mt) REVERT: 5 44 PHE cc_start: 0.6289 (t80) cc_final: 0.5746 (t80) REVERT: 6 79 ASN cc_start: 0.7909 (t0) cc_final: 0.7682 (t0) REVERT: 6 171 PHE cc_start: 0.8409 (t80) cc_final: 0.7975 (t80) REVERT: 7 483 LEU cc_start: 0.8948 (mt) cc_final: 0.8621 (tt) REVERT: 7 494 MET cc_start: 0.6723 (mmp) cc_final: 0.6470 (mmt) REVERT: 7 644 LEU cc_start: 0.9009 (mt) cc_final: 0.8806 (mt) outliers start: 8 outliers final: 3 residues processed: 497 average time/residue: 0.3555 time to fit residues: 271.4988 Evaluate side-chains 369 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 366 time to evaluate : 3.012 ------------------------------------------------------------------------------- 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: 2.9990 chunk 192 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 272 optimal weight: 0.6980 chunk 134 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 474 HIS 2 18 ASN ** 2 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 289 ASN ** 2 362 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 63 HIS ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 265 GLN ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 355 GLN ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 187 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24210 Z= 0.352 Angle : 0.706 11.685 32915 Z= 0.359 Chirality : 0.044 0.248 3711 Planarity : 0.005 0.076 4050 Dihedral : 12.140 173.566 3539 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 0.12 % Allowed : 5.51 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2768 helix: 0.35 (0.14), residues: 1346 sheet: -2.13 (0.27), residues: 305 loop : -1.18 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 2 156 HIS 0.016 0.002 HIS 1 524 PHE 0.025 0.002 PHE 2 45 TYR 0.028 0.002 TYR 0 410 ARG 0.015 0.001 ARG 2 58 *********************** 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 478 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 475 time to evaluate : 2.768 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: 0 264 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6808 (mt-10) REVERT: 0 279 GLN cc_start: 0.7531 (tp-100) cc_final: 0.7107 (tp-100) REVERT: 0 345 ARG cc_start: 0.7148 (ptp-110) cc_final: 0.5718 (ttm170) REVERT: 0 596 LEU cc_start: 0.9356 (tp) cc_final: 0.9101 (tt) REVERT: 0 659 HIS cc_start: 0.7236 (t70) cc_final: 0.6840 (t70) REVERT: 1 117 MET cc_start: 0.5626 (ppp) cc_final: 0.4055 (tpt) REVERT: 1 499 ARG cc_start: 0.5797 (mtt180) cc_final: 0.5518 (mtt180) REVERT: 2 73 LEU cc_start: 0.8316 (pp) cc_final: 0.7918 (tp) REVERT: 2 98 THR cc_start: 0.5760 (t) cc_final: 0.5443 (m) REVERT: 2 323 LEU cc_start: 0.8992 (tp) cc_final: 0.8741 (tp) REVERT: 2 365 ILE cc_start: 0.8753 (pt) cc_final: 0.8295 (tp) REVERT: 2 408 LEU cc_start: 0.7550 (tp) cc_final: 0.7229 (tp) REVERT: 2 448 HIS cc_start: 0.6843 (t-90) cc_final: 0.6427 (t-170) REVERT: 5 44 PHE cc_start: 0.6417 (t80) cc_final: 0.5915 (t80) REVERT: 6 101 ILE cc_start: 0.8117 (pt) cc_final: 0.7882 (pt) REVERT: 6 171 PHE cc_start: 0.8338 (t80) cc_final: 0.7947 (t80) REVERT: 7 153 MET cc_start: 0.6733 (mmp) cc_final: 0.6181 (mmt) REVERT: 7 483 LEU cc_start: 0.8872 (mt) cc_final: 0.8581 (tt) REVERT: 7 494 MET cc_start: 0.6487 (mmp) cc_final: 0.6070 (mmm) REVERT: 7 504 LYS cc_start: 0.8175 (tppp) cc_final: 0.7975 (tttt) outliers start: 3 outliers final: 1 residues processed: 476 average time/residue: 0.3511 time to fit residues: 258.7646 Evaluate side-chains 348 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 347 time to evaluate : 2.729 ------------------------------------------------------------------------------- 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: 10.0000 chunk 154 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 0.0070 chunk 232 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 145 GLN 0 148 HIS ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 264 HIS 2 362 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 4 145 HIS 6 265 GLN ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 187 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** ** 7 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 677 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24210 Z= 0.206 Angle : 0.635 10.634 32915 Z= 0.324 Chirality : 0.043 0.218 3711 Planarity : 0.004 0.067 4050 Dihedral : 12.041 173.406 3539 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2768 helix: 0.52 (0.14), residues: 1351 sheet: -2.03 (0.28), residues: 298 loop : -1.06 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP 4 229 HIS 0.018 0.001 HIS 7 187 PHE 0.026 0.002 PHE 3 58 TYR 0.043 0.002 TYR 3 125 ARG 0.006 0.001 ARG 7 62 *********************** 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 508 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 506 time to evaluate : 2.923 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: 0 86 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7694 (mt-10) REVERT: 0 264 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6985 (mt-10) REVERT: 0 279 GLN cc_start: 0.7442 (tp-100) cc_final: 0.7147 (tp-100) REVERT: 0 345 ARG cc_start: 0.7006 (ptp-110) cc_final: 0.5304 (ttm110) REVERT: 0 490 LEU cc_start: 0.8501 (pp) cc_final: 0.8128 (pp) REVERT: 0 596 LEU cc_start: 0.9297 (tp) cc_final: 0.9057 (tt) REVERT: 0 657 MET cc_start: 0.8646 (mmp) cc_final: 0.7912 (tpp) REVERT: 0 659 HIS cc_start: 0.6887 (t70) cc_final: 0.6520 (t70) REVERT: 1 117 MET cc_start: 0.5582 (ppp) cc_final: 0.4008 (tpt) REVERT: 1 499 ARG cc_start: 0.5667 (mtt180) cc_final: 0.5258 (mtt180) REVERT: 2 73 LEU cc_start: 0.8119 (pp) cc_final: 0.7624 (tp) REVERT: 2 203 PHE cc_start: 0.8635 (t80) cc_final: 0.8435 (t80) REVERT: 2 266 ARG cc_start: 0.7006 (tmm160) cc_final: 0.6689 (ptt90) REVERT: 2 323 LEU cc_start: 0.8972 (tp) cc_final: 0.8769 (tp) REVERT: 2 448 HIS cc_start: 0.6789 (t-90) cc_final: 0.6407 (t-170) REVERT: 3 75 ARG cc_start: 0.7123 (mtm180) cc_final: 0.6685 (mtm180) REVERT: 5 44 PHE cc_start: 0.6207 (t80) cc_final: 0.5746 (t80) REVERT: 6 104 ILE cc_start: 0.8748 (tt) cc_final: 0.8389 (tt) REVERT: 7 446 ILE cc_start: 0.8496 (mm) cc_final: 0.8270 (mm) REVERT: 7 483 LEU cc_start: 0.8852 (mt) cc_final: 0.8521 (tt) REVERT: 7 494 MET cc_start: 0.6394 (mmp) cc_final: 0.6052 (mmm) REVERT: 7 505 VAL cc_start: 0.8678 (t) cc_final: 0.8366 (t) REVERT: 7 571 TYR cc_start: 0.5356 (m-80) cc_final: 0.4986 (m-10) REVERT: 7 634 ARG cc_start: 0.8840 (tmm-80) cc_final: 0.8591 (tmm-80) outliers start: 2 outliers final: 2 residues processed: 507 average time/residue: 0.3532 time to fit residues: 277.6445 Evaluate side-chains 366 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 364 time to evaluate : 2.903 ------------------------------------------------------------------------------- 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: 0.7980 chunk 245 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 67 optimal weight: 0.0970 chunk 272 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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** 0 519 ASN ** 0 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 264 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN 4 240 GLN ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 112 HIS ** 7 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 377 GLN ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 629 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 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 : 0.003 0.039 24210 Z= 0.220 Angle : 0.617 8.278 32915 Z= 0.315 Chirality : 0.042 0.285 3711 Planarity : 0.005 0.093 4050 Dihedral : 12.050 174.523 3539 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % 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: 2768 helix: 0.55 (0.14), residues: 1358 sheet: -1.99 (0.29), residues: 282 loop : -1.11 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP 2 96 HIS 0.020 0.001 HIS 7 187 PHE 0.029 0.002 PHE 1 125 TYR 0.019 0.002 TYR 6 90 ARG 0.013 0.001 ARG 2 58 *********************** 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 486 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 484 time to evaluate : 2.868 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: 0 1 MET cc_start: 0.3732 (ttm) cc_final: 0.1791 (tpt) REVERT: 0 207 TYR cc_start: 0.7489 (p90) cc_final: 0.7217 (p90) REVERT: 0 264 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6692 (mt-10) REVERT: 0 279 GLN cc_start: 0.7372 (tp-100) cc_final: 0.7092 (tp-100) REVERT: 0 345 ARG cc_start: 0.6760 (ptp-110) cc_final: 0.5497 (ttm170) REVERT: 0 432 ILE cc_start: 0.7935 (tt) cc_final: 0.7501 (mp) REVERT: 0 490 LEU cc_start: 0.8574 (pp) cc_final: 0.8223 (pp) REVERT: 0 596 LEU cc_start: 0.9327 (tp) cc_final: 0.9116 (tt) REVERT: 0 659 HIS cc_start: 0.6717 (t70) cc_final: 0.6455 (t70) REVERT: 1 117 MET cc_start: 0.5700 (ppp) cc_final: 0.4164 (tpt) REVERT: 1 499 ARG cc_start: 0.5715 (mtt180) cc_final: 0.5423 (mtt180) REVERT: 2 73 LEU cc_start: 0.8213 (pp) cc_final: 0.7795 (tp) REVERT: 2 266 ARG cc_start: 0.7108 (tmm160) cc_final: 0.6841 (ptt90) REVERT: 2 323 LEU cc_start: 0.8955 (tp) cc_final: 0.8740 (tp) REVERT: 2 335 LEU cc_start: 0.8330 (mt) cc_final: 0.8040 (mm) REVERT: 2 408 LEU cc_start: 0.7720 (tp) cc_final: 0.7350 (tp) REVERT: 2 448 HIS cc_start: 0.6816 (t-90) cc_final: 0.6450 (t-170) REVERT: 3 21 LEU cc_start: 0.6714 (tp) cc_final: 0.5826 (tp) REVERT: 3 75 ARG cc_start: 0.7238 (mtm180) cc_final: 0.6619 (mtm180) REVERT: 3 99 LEU cc_start: 0.8120 (mp) cc_final: 0.7886 (mp) REVERT: 4 38 ILE cc_start: 0.9044 (mt) cc_final: 0.8681 (mt) REVERT: 5 44 PHE cc_start: 0.6080 (t80) cc_final: 0.5315 (t80) REVERT: 6 101 ILE cc_start: 0.7917 (pt) cc_final: 0.7672 (pt) REVERT: 6 104 ILE cc_start: 0.8754 (tt) cc_final: 0.8396 (tt) REVERT: 7 446 ILE cc_start: 0.8500 (mm) cc_final: 0.8257 (mm) REVERT: 7 483 LEU cc_start: 0.8822 (mt) cc_final: 0.8564 (tt) REVERT: 7 494 MET cc_start: 0.6334 (mmp) cc_final: 0.5959 (mmm) REVERT: 7 571 TYR cc_start: 0.5235 (m-80) cc_final: 0.4927 (m-80) REVERT: 7 634 ARG cc_start: 0.8852 (tmm-80) cc_final: 0.8563 (tmm-80) outliers start: 2 outliers final: 1 residues processed: 485 average time/residue: 0.3498 time to fit residues: 264.8934 Evaluate side-chains 364 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 363 time to evaluate : 2.805 ------------------------------------------------------------------------------- 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: 0.6980 chunk 30 optimal weight: 2.9990 chunk 155 optimal weight: 0.0070 chunk 199 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 271 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 328 HIS ** 0 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 377 GLN ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24210 Z= 0.205 Angle : 0.628 10.496 32915 Z= 0.320 Chirality : 0.042 0.236 3711 Planarity : 0.004 0.062 4050 Dihedral : 12.033 174.657 3539 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2768 helix: 0.52 (0.14), residues: 1358 sheet: -1.90 (0.29), residues: 278 loop : -1.13 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 2 96 HIS 0.016 0.001 HIS 7 187 PHE 0.028 0.002 PHE 3 58 TYR 0.049 0.002 TYR 3 125 ARG 0.009 0.000 ARG 2 58 *********************** 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 470 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 470 time to evaluate : 2.958 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: 0 1 MET cc_start: 0.3556 (ttm) cc_final: 0.1579 (tpt) REVERT: 0 264 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6982 (mt-10) REVERT: 0 279 GLN cc_start: 0.7424 (tp-100) cc_final: 0.7141 (tp-100) REVERT: 0 345 ARG cc_start: 0.6655 (ptp-110) cc_final: 0.5158 (ttm170) REVERT: 0 596 LEU cc_start: 0.9300 (tp) cc_final: 0.9087 (tt) REVERT: 0 657 MET cc_start: 0.8661 (mmp) cc_final: 0.7922 (tpp) REVERT: 0 659 HIS cc_start: 0.6730 (t70) cc_final: 0.6367 (t70) REVERT: 1 117 MET cc_start: 0.5528 (ppp) cc_final: 0.4282 (tpp) REVERT: 1 499 ARG cc_start: 0.5518 (mtt180) cc_final: 0.5251 (mtt180) REVERT: 2 41 CYS cc_start: 0.8535 (m) cc_final: 0.7649 (p) REVERT: 2 73 LEU cc_start: 0.8179 (pp) cc_final: 0.7917 (tp) REVERT: 2 323 LEU cc_start: 0.8993 (tp) cc_final: 0.8644 (tp) REVERT: 2 335 LEU cc_start: 0.8289 (mt) cc_final: 0.7948 (mm) REVERT: 2 408 LEU cc_start: 0.7475 (tp) cc_final: 0.5811 (tp) REVERT: 2 448 HIS cc_start: 0.6818 (t-90) cc_final: 0.6533 (t-170) REVERT: 3 75 ARG cc_start: 0.7211 (mtm180) cc_final: 0.6745 (mtm180) REVERT: 5 44 PHE cc_start: 0.6030 (t80) cc_final: 0.4663 (t80) REVERT: 6 72 GLU cc_start: 0.6627 (tp30) cc_final: 0.6385 (tp30) REVERT: 6 104 ILE cc_start: 0.8760 (tt) cc_final: 0.8485 (tt) REVERT: 6 171 PHE cc_start: 0.8203 (t80) cc_final: 0.7916 (t80) REVERT: 7 446 ILE cc_start: 0.8505 (mm) cc_final: 0.8258 (mm) REVERT: 7 483 LEU cc_start: 0.8849 (mt) cc_final: 0.8602 (tt) REVERT: 7 494 MET cc_start: 0.6263 (mmp) cc_final: 0.5939 (mmm) REVERT: 7 571 TYR cc_start: 0.5203 (m-80) cc_final: 0.4903 (m-10) REVERT: 7 634 ARG cc_start: 0.8758 (tmm-80) cc_final: 0.8424 (tmm-80) REVERT: 7 661 SER cc_start: 0.8587 (t) cc_final: 0.8349 (t) REVERT: 7 662 LEU cc_start: 0.8553 (mt) cc_final: 0.8282 (mt) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.3571 time to fit residues: 265.1394 Evaluate side-chains 349 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 2.698 ------------------------------------------------------------------------------- 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: 0.7980 chunk 108 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** ** 0 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 264 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 6 227 HIS ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 190 GLN 7 377 GLN ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.5542 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= 0.243 Angle : 0.644 12.313 32915 Z= 0.329 Chirality : 0.043 0.324 3711 Planarity : 0.005 0.114 4050 Dihedral : 12.094 175.364 3539 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2768 helix: 0.49 (0.14), residues: 1359 sheet: -1.94 (0.29), residues: 289 loop : -1.13 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP 1 221 HIS 0.016 0.001 HIS 7 187 PHE 0.045 0.002 PHE 3 39 TYR 0.033 0.002 TYR 0 584 ARG 0.007 0.001 ARG 2 400 *********************** 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 463 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 2.475 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: 0 74 SER cc_start: 0.8074 (t) cc_final: 0.7842 (t) REVERT: 0 207 TYR cc_start: 0.7585 (p90) cc_final: 0.7315 (p90) REVERT: 0 264 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6993 (mt-10) REVERT: 0 279 GLN cc_start: 0.7581 (tp-100) cc_final: 0.7304 (tp-100) REVERT: 0 342 TRP cc_start: 0.5237 (t60) cc_final: 0.5008 (t60) REVERT: 0 596 LEU cc_start: 0.9296 (tp) cc_final: 0.9077 (tt) REVERT: 0 606 GLU cc_start: 0.5058 (pm20) cc_final: 0.4583 (pm20) REVERT: 1 117 MET cc_start: 0.5579 (ppp) cc_final: 0.4335 (tpp) REVERT: 1 499 ARG cc_start: 0.5524 (mtt180) cc_final: 0.5143 (mtt180) REVERT: 2 41 CYS cc_start: 0.8621 (m) cc_final: 0.7688 (p) REVERT: 2 73 LEU cc_start: 0.8264 (pp) cc_final: 0.7818 (tp) REVERT: 2 174 ASP cc_start: 0.7404 (p0) cc_final: 0.7033 (p0) REVERT: 2 313 TYR cc_start: 0.8433 (m-80) cc_final: 0.8119 (m-80) REVERT: 2 323 LEU cc_start: 0.8989 (tp) cc_final: 0.8655 (tp) REVERT: 2 335 LEU cc_start: 0.8344 (mt) cc_final: 0.8078 (mm) REVERT: 2 448 HIS cc_start: 0.6831 (t-90) cc_final: 0.6590 (t-170) REVERT: 3 75 ARG cc_start: 0.7198 (mtm180) cc_final: 0.6694 (mtm180) REVERT: 3 99 LEU cc_start: 0.8041 (mp) cc_final: 0.7707 (mp) REVERT: 5 44 PHE cc_start: 0.5836 (t80) cc_final: 0.5302 (t80) REVERT: 6 72 GLU cc_start: 0.6768 (tp30) cc_final: 0.6499 (tp30) REVERT: 6 104 ILE cc_start: 0.8771 (tt) cc_final: 0.8371 (tt) REVERT: 6 171 PHE cc_start: 0.8222 (t80) cc_final: 0.7871 (t80) REVERT: 7 446 ILE cc_start: 0.8479 (mm) cc_final: 0.8276 (mm) REVERT: 7 494 MET cc_start: 0.6278 (mmp) cc_final: 0.5972 (mmm) REVERT: 7 505 VAL cc_start: 0.8335 (t) cc_final: 0.8128 (t) REVERT: 7 571 TYR cc_start: 0.5277 (m-80) cc_final: 0.4970 (m-80) REVERT: 7 661 SER cc_start: 0.8524 (t) cc_final: 0.8319 (t) REVERT: 7 662 LEU cc_start: 0.8593 (mt) cc_final: 0.8328 (mt) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.3371 time to fit residues: 246.4440 Evaluate side-chains 352 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 2.894 ------------------------------------------------------------------------------- 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: 0.6980 chunk 260 optimal weight: 0.8980 chunk 237 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 77 optimal weight: 30.0000 chunk 228 optimal weight: 0.2980 chunk 239 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 377 GLN ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.5686 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= 0.229 Angle : 0.652 10.759 32915 Z= 0.331 Chirality : 0.043 0.271 3711 Planarity : 0.004 0.059 4050 Dihedral : 12.110 175.412 3539 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -0.73 (0.16), residues: 2768 helix: 0.46 (0.14), residues: 1363 sheet: -1.87 (0.28), residues: 294 loop : -1.17 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP 1 221 HIS 0.021 0.002 HIS 0 328 PHE 0.028 0.002 PHE 3 58 TYR 0.047 0.002 TYR 3 125 ARG 0.008 0.001 ARG 3 93 *********************** 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 453 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 2.970 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: 0 264 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7011 (mt-10) REVERT: 0 279 GLN cc_start: 0.7584 (tp-100) cc_final: 0.7315 (tp-100) REVERT: 0 606 GLU cc_start: 0.5067 (pm20) cc_final: 0.4608 (pm20) REVERT: 0 657 MET cc_start: 0.8557 (mmp) cc_final: 0.7783 (tpp) REVERT: 1 117 MET cc_start: 0.5530 (ppp) cc_final: 0.4313 (tpp) REVERT: 1 499 ARG cc_start: 0.5697 (mtt180) cc_final: 0.5371 (mtt180) REVERT: 1 525 ILE cc_start: 0.8123 (mp) cc_final: 0.7896 (mm) REVERT: 2 41 CYS cc_start: 0.8587 (m) cc_final: 0.7689 (p) REVERT: 2 73 LEU cc_start: 0.8263 (pp) cc_final: 0.7807 (tp) REVERT: 2 174 ASP cc_start: 0.7433 (p0) cc_final: 0.7094 (p0) REVERT: 2 323 LEU cc_start: 0.8960 (tp) cc_final: 0.8644 (tp) REVERT: 2 439 ARG cc_start: 0.6419 (mmm160) cc_final: 0.6177 (mmm160) REVERT: 3 75 ARG cc_start: 0.7208 (mtm180) cc_final: 0.6680 (mtm180) REVERT: 3 99 LEU cc_start: 0.8093 (mp) cc_final: 0.7854 (mp) REVERT: 5 44 PHE cc_start: 0.6149 (t80) cc_final: 0.5437 (t80) REVERT: 6 72 GLU cc_start: 0.6758 (tp30) cc_final: 0.6525 (tp30) REVERT: 6 104 ILE cc_start: 0.8775 (tt) cc_final: 0.8440 (tt) REVERT: 6 171 PHE cc_start: 0.8232 (t80) cc_final: 0.7863 (t80) REVERT: 7 446 ILE cc_start: 0.8446 (mm) cc_final: 0.8216 (mm) REVERT: 7 494 MET cc_start: 0.6234 (mmp) cc_final: 0.5943 (mmm) REVERT: 7 505 VAL cc_start: 0.8368 (t) cc_final: 0.8132 (t) REVERT: 7 571 TYR cc_start: 0.5252 (m-80) cc_final: 0.4886 (m-80) REVERT: 7 662 LEU cc_start: 0.8614 (mt) cc_final: 0.8369 (mt) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.3387 time to fit residues: 241.1656 Evaluate side-chains 350 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 2.549 ------------------------------------------------------------------------------- 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: 0.1980 chunk 267 optimal weight: 0.3980 chunk 163 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 280 optimal weight: 4.9990 chunk 258 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 264 HIS ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 ASN 4 237 GLN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 377 GLN ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24210 Z= 0.241 Angle : 0.659 9.003 32915 Z= 0.336 Chirality : 0.043 0.221 3711 Planarity : 0.004 0.058 4050 Dihedral : 12.144 175.791 3539 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.27 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 2768 helix: 0.44 (0.14), residues: 1359 sheet: -1.87 (0.28), residues: 299 loop : -1.16 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP 2 96 HIS 0.022 0.002 HIS 0 328 PHE 0.023 0.002 PHE 7 378 TYR 0.040 0.002 TYR 3 125 ARG 0.006 0.001 ARG 2 400 ********************** 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 449 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 2.799 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: 0 264 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6913 (mt-10) REVERT: 0 279 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7353 (tp-100) REVERT: 0 657 MET cc_start: 0.8553 (mmp) cc_final: 0.7748 (tpp) REVERT: 1 117 MET cc_start: 0.5636 (ppp) cc_final: 0.4463 (tpp) REVERT: 1 499 ARG cc_start: 0.5461 (mtt180) cc_final: 0.5108 (mtt180) REVERT: 2 41 CYS cc_start: 0.8609 (m) cc_final: 0.7656 (p) REVERT: 2 73 LEU cc_start: 0.8256 (pp) cc_final: 0.7783 (tp) REVERT: 2 174 ASP cc_start: 0.7481 (p0) cc_final: 0.7104 (p0) REVERT: 2 323 LEU cc_start: 0.8950 (tp) cc_final: 0.8631 (tp) REVERT: 3 21 LEU cc_start: 0.5653 (tp) cc_final: 0.5337 (tt) REVERT: 3 39 PHE cc_start: 0.5167 (m-10) cc_final: 0.4895 (m-80) REVERT: 3 75 ARG cc_start: 0.7290 (mtm180) cc_final: 0.6757 (mtm180) REVERT: 3 99 LEU cc_start: 0.8242 (mp) cc_final: 0.7916 (mp) REVERT: 5 44 PHE cc_start: 0.6143 (t80) cc_final: 0.5512 (t80) REVERT: 6 72 GLU cc_start: 0.6794 (tp30) cc_final: 0.6571 (tp30) REVERT: 6 104 ILE cc_start: 0.8762 (tt) cc_final: 0.8396 (tt) REVERT: 6 171 PHE cc_start: 0.8300 (t80) cc_final: 0.7744 (t80) REVERT: 6 331 PHE cc_start: 0.6526 (m-10) cc_final: 0.6256 (m-80) REVERT: 7 446 ILE cc_start: 0.8458 (mm) cc_final: 0.8253 (mm) REVERT: 7 571 TYR cc_start: 0.5262 (m-80) cc_final: 0.4908 (m-80) REVERT: 7 661 SER cc_start: 0.8579 (t) cc_final: 0.8307 (t) REVERT: 7 662 LEU cc_start: 0.8603 (mt) cc_final: 0.8257 (mt) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.3369 time to fit residues: 237.9920 Evaluate side-chains 343 residues out of total 2503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 2.720 ------------------------------------------------------------------------------- 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: 0.7980 chunk 238 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 230 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 114 ASN ** 0 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 179 ASN ** 4 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 6 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 377 GLN ** 7 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 677 GLN ** W 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.142980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123637 restraints weight = 57084.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.123236 restraints weight = 100088.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.123706 restraints weight = 95545.899| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24210 Z= 0.234 Angle : 0.654 10.657 32915 Z= 0.331 Chirality : 0.043 0.214 3711 Planarity : 0.004 0.057 4050 Dihedral : 12.165 175.880 3539 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -0.73 (0.16), residues: 2768 helix: 0.46 (0.14), residues: 1361 sheet: -1.81 (0.29), residues: 288 loop : -1.21 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP 2 96 HIS 0.019 0.002 HIS 0 328 PHE 0.032 0.002 PHE 3 58 TYR 0.022 0.002 TYR 0 639 ARG 0.006 0.000 ARG 2 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5736.56 seconds wall clock time: 104 minutes 17.76 seconds (6257.76 seconds total)