Starting phenix.real_space_refine on Tue Mar 19 04:55:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efh_28082/03_2024/8efh_28082_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efh_28082/03_2024/8efh_28082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efh_28082/03_2024/8efh_28082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efh_28082/03_2024/8efh_28082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efh_28082/03_2024/8efh_28082_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efh_28082/03_2024/8efh_28082_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 138 5.16 5 C 14639 2.51 5 N 3941 2.21 5 O 4492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 211": "OD1" <-> "OD2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "P TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23228 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5918 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 28, 'TRANS': 705} Chain breaks: 3 Chain: "F" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "B" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "C" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "E" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "O" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "P" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1326 Classifications: {'peptide': 166} Link IDs: {'TRANS': 165} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.69, per 1000 atoms: 0.50 Number of scatterers: 23228 At special positions: 0 Unit cell: (162.778, 100.254, 249.018, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 12 15.00 Mg 6 11.99 O 4492 8.00 N 3941 7.00 C 14639 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: 8.95 Conformation dependent library (CDL) restraints added in 3.9 seconds 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 129 helices and 29 sheets defined 49.1% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.97 Creating SS restraints... Processing helix chain 'A' and resid 14 through 16 No H-bonds generated for 'chain 'A' and resid 14 through 16' Processing helix chain 'A' and resid 23 through 26 No H-bonds generated for 'chain 'A' and resid 23 through 26' Processing helix chain 'A' and resid 98 through 110 removed outlier: 4.042A pdb=" N LEU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 136 through 142 Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 217 through 230 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 311 through 314 No H-bonds generated for 'chain 'A' and resid 311 through 314' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 417 through 447 Processing helix chain 'A' and resid 473 through 504 Processing helix chain 'A' and resid 518 through 525 Processing helix chain 'A' and resid 530 through 538 Processing helix chain 'A' and resid 545 through 556 Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 604 through 611 removed outlier: 3.563A pdb=" N LYS A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 619 No H-bonds generated for 'chain 'A' and resid 616 through 619' Processing helix chain 'A' and resid 647 through 664 removed outlier: 4.271A pdb=" N SER A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 698 through 707 Processing helix chain 'A' and resid 715 through 726 removed outlier: 4.137A pdb=" N ARG A 723 " --> pdb=" O ARG A 719 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 724 " --> pdb=" O GLN A 720 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU A 725 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASN A 726 " --> pdb=" O TYR A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.591A pdb=" N LEU A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 780 removed outlier: 3.603A pdb=" N GLU A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 193 Processing helix chain 'F' and resid 203 through 216 removed outlier: 3.980A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 252 through 256 removed outlier: 3.716A pdb=" N ARG F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 284 removed outlier: 3.789A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 296 Processing helix chain 'F' and resid 302 through 305 Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 338 through 348 Processing helix chain 'F' and resid 353 through 355 No H-bonds generated for 'chain 'F' and resid 353 through 355' Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 367 through 371 removed outlier: 3.852A pdb=" N VAL F 370 " --> pdb=" O PRO F 367 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS F 371 " --> pdb=" O SER F 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 367 through 371' Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.552A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.590A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.986A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.892A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 348 Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.787A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.736A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.581A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 4.075A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.940A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 260 No H-bonds generated for 'chain 'C' and resid 258 through 260' Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.760A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 removed outlier: 4.019A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 371' Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 144 removed outlier: 3.700A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.814A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.952A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.596A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.845A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 296 Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.741A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 348 Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.567A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 371 Proline residue: D 367 - end of helix removed outlier: 5.376A pdb=" N VAL D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.672A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 256 removed outlier: 3.622A pdb=" N PHE E 255 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 256' Processing helix chain 'E' and resid 258 through 261 removed outlier: 3.510A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 258 through 261' Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 removed outlier: 4.119A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 296 Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 338 through 347 Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.980A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 371 Proline residue: E 367 - end of helix removed outlier: 5.443A pdb=" N VAL E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 209 removed outlier: 4.184A pdb=" N GLN O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 209 removed outlier: 3.623A pdb=" N ARG P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA P 209 " --> pdb=" O LYS P 205 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 39 Processing sheet with id= B, first strand: chain 'A' and resid 58 through 60 Processing sheet with id= C, first strand: chain 'A' and resid 115 through 118 removed outlier: 4.108A pdb=" N PHE A 121 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N CYS A 122 " --> pdb=" O PRO A 667 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE A 669 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR A 124 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG A 671 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 178 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 246 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 260 " --> pdb=" O HIS A 251 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 403 through 406 Processing sheet with id= E, first strand: chain 'A' and resid 577 through 580 removed outlier: 4.193A pdb=" N PHE A 577 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.829A pdb=" N ILE A 713 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 763 " --> pdb=" O ILE A 713 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 8 through 11 Processing sheet with id= H, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.631A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 103 through 107 Processing sheet with id= J, first strand: chain 'F' and resid 298 through 300 removed outlier: 3.541A pdb=" N SER F 155 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 238 through 240 Processing sheet with id= L, first strand: chain 'B' and resid 29 through 31 removed outlier: 7.437A pdb=" N CYS B 10 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= N, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.818A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 238 through 240 Processing sheet with id= P, first strand: chain 'C' and resid 17 through 19 Processing sheet with id= Q, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= R, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= S, first strand: chain 'C' and resid 298 through 300 Processing sheet with id= T, first strand: chain 'C' and resid 238 through 240 removed outlier: 3.537A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.692A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 34 through 38 Processing sheet with id= W, first strand: chain 'D' and resid 298 through 300 removed outlier: 3.555A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 238 through 240 Processing sheet with id= Y, first strand: chain 'E' and resid 8 through 11 Processing sheet with id= Z, first strand: chain 'E' and resid 35 through 38 removed outlier: 3.616A pdb=" N VAL E 35 " --> pdb=" O LYS E 68 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= AB, first strand: chain 'E' and resid 298 through 300 removed outlier: 3.586A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 238 through 240 1077 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.43 Time building geometry restraints manager: 9.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7644 1.34 - 1.46: 4886 1.46 - 1.58: 10890 1.58 - 1.70: 18 1.70 - 1.82: 241 Bond restraints: 23679 Sorted by residual: bond pdb=" CD GLU P 131 " pdb=" OE1 GLU P 131 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.72e+00 bond pdb=" CG GLU P 131 " pdb=" CD GLU P 131 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.51e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 23674 not shown) Histogram of bond angle deviations from ideal: 98.48 - 106.02: 581 106.02 - 113.56: 13043 113.56 - 121.10: 12185 121.10 - 128.64: 6074 128.64 - 136.18: 134 Bond angle restraints: 32017 Sorted by residual: angle pdb=" N GLU P 131 " pdb=" CA GLU P 131 " pdb=" CB GLU P 131 " ideal model delta sigma weight residual 110.39 117.07 -6.68 1.66e+00 3.63e-01 1.62e+01 angle pdb=" C ILE P 130 " pdb=" N GLU P 131 " pdb=" CA GLU P 131 " ideal model delta sigma weight residual 120.72 114.13 6.59 1.67e+00 3.59e-01 1.56e+01 angle pdb=" CB ARG P 133 " pdb=" CG ARG P 133 " pdb=" CD ARG P 133 " ideal model delta sigma weight residual 111.30 118.96 -7.66 2.30e+00 1.89e-01 1.11e+01 angle pdb=" C GLU O 138 " pdb=" N GLU O 139 " pdb=" CA GLU O 139 " ideal model delta sigma weight residual 120.72 115.22 5.50 1.67e+00 3.59e-01 1.08e+01 angle pdb=" CA GLU P 131 " pdb=" CB GLU P 131 " pdb=" CG GLU P 131 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 ... (remaining 32012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 14100 35.11 - 70.22: 269 70.22 - 105.32: 21 105.32 - 140.43: 6 140.43 - 175.54: 11 Dihedral angle restraints: 14407 sinusoidal: 5921 harmonic: 8486 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 115.54 -175.54 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP A2002 " pdb=" O5' ADP A2002 " pdb=" PA ADP A2002 " pdb=" O2A ADP A2002 " ideal model delta sinusoidal sigma weight residual -60.00 109.41 -169.41 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 99.62 -159.61 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 14404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2394 0.035 - 0.070: 779 0.070 - 0.104: 272 0.104 - 0.139: 90 0.139 - 0.174: 6 Chirality restraints: 3541 Sorted by residual: chirality pdb=" CB ILE A 580 " pdb=" CA ILE A 580 " pdb=" CG1 ILE A 580 " pdb=" CG2 ILE A 580 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CB ILE P 130 " pdb=" CA ILE P 130 " pdb=" CG1 ILE P 130 " pdb=" CG2 ILE P 130 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.79e-01 chirality pdb=" CA GLU P 131 " pdb=" N GLU P 131 " pdb=" C GLU P 131 " pdb=" CB GLU P 131 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 3538 not shown) Planarity restraints: 4122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 366 " -0.041 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO C 367 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET P 127 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C MET P 127 " 0.039 2.00e-02 2.50e+03 pdb=" O MET P 127 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS P 128 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 111 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO D 112 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " -0.028 5.00e-02 4.00e+02 ... (remaining 4119 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 201 2.63 - 3.20: 20576 3.20 - 3.76: 35687 3.76 - 4.33: 48150 4.33 - 4.90: 80933 Nonbonded interactions: 185547 Sorted by model distance: nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.060 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.067 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.111 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.117 2.170 nonbonded pdb=" O3B ADP F 401 " pdb="MG MG F 402 " model vdw 2.121 2.170 ... (remaining 185542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'O' selection = chain 'P' } 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 individual isotropic 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: 5.810 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: 18.140 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 59.730 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 0.040 23679 Z= 0.155 Angle : 0.544 8.626 32017 Z= 0.276 Chirality : 0.041 0.174 3541 Planarity : 0.004 0.063 4122 Dihedral : 15.521 175.539 8945 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.16), residues: 2899 helix: 1.88 (0.15), residues: 1362 sheet: 0.12 (0.26), residues: 435 loop : -0.27 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 79 HIS 0.003 0.001 HIS C 73 PHE 0.029 0.001 PHE A 359 TYR 0.028 0.001 TYR P 162 ARG 0.008 0.000 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8424 (ppp) cc_final: 0.8194 (ppp) REVERT: C 143 TYR cc_start: 0.8462 (m-80) cc_final: 0.8194 (m-80) REVERT: D 47 MET cc_start: 0.6811 (tpt) cc_final: 0.5912 (ptp) REVERT: O 130 ILE cc_start: 0.8223 (tp) cc_final: 0.7965 (tt) REVERT: P 89 ASN cc_start: 0.7904 (m-40) cc_final: 0.7582 (m-40) REVERT: P 93 GLN cc_start: 0.7888 (mp-120) cc_final: 0.7647 (mp10) REVERT: P 175 ASP cc_start: 0.8314 (m-30) cc_final: 0.7990 (m-30) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.3451 time to fit residues: 121.4961 Evaluate side-chains 188 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 263 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23679 Z= 0.286 Angle : 0.575 7.958 32017 Z= 0.286 Chirality : 0.044 0.157 3541 Planarity : 0.004 0.050 4122 Dihedral : 11.584 172.868 3238 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.52 % Allowed : 7.26 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2899 helix: 1.58 (0.14), residues: 1427 sheet: -0.26 (0.25), residues: 438 loop : -0.81 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 130 HIS 0.007 0.001 HIS D 73 PHE 0.025 0.001 PHE A 46 TYR 0.023 0.001 TYR P 162 ARG 0.008 0.000 ARG P 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8347 (ppp) cc_final: 0.8112 (ppp) REVERT: C 143 TYR cc_start: 0.8576 (m-80) cc_final: 0.8326 (m-80) REVERT: D 47 MET cc_start: 0.7057 (tpt) cc_final: 0.6077 (ptp) REVERT: E 223 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: O 127 MET cc_start: 0.7377 (ttm) cc_final: 0.6852 (tpt) outliers start: 13 outliers final: 7 residues processed: 210 average time/residue: 0.3927 time to fit residues: 130.0050 Evaluate side-chains 196 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 146 optimal weight: 0.0170 chunk 81 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 72 optimal weight: 30.0000 chunk 263 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 211 optimal weight: 0.7980 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 HIS ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23679 Z= 0.225 Angle : 0.539 7.167 32017 Z= 0.266 Chirality : 0.043 0.168 3541 Planarity : 0.004 0.043 4122 Dihedral : 11.430 178.696 3238 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.08 % Allowed : 9.19 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2899 helix: 1.61 (0.14), residues: 1431 sheet: -0.18 (0.24), residues: 433 loop : -0.86 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 130 HIS 0.005 0.001 HIS F 88 PHE 0.018 0.001 PHE A 46 TYR 0.022 0.001 TYR P 162 ARG 0.003 0.000 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 197 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.5297 (pmm) cc_final: 0.4873 (pmm) REVERT: A 77 MET cc_start: 0.8286 (ppp) cc_final: 0.8054 (ppp) REVERT: F 107 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: C 143 TYR cc_start: 0.8549 (m-80) cc_final: 0.8320 (m-80) REVERT: D 47 MET cc_start: 0.7089 (tpt) cc_final: 0.5926 (ptp) REVERT: D 325 MET cc_start: 0.8171 (tpt) cc_final: 0.7711 (tpt) REVERT: E 227 MET cc_start: 0.7735 (mmm) cc_final: 0.7452 (mmm) REVERT: O 127 MET cc_start: 0.7488 (ttm) cc_final: 0.6857 (tpt) REVERT: P 127 MET cc_start: 0.6653 (mtp) cc_final: 0.6154 (mmm) REVERT: P 141 MET cc_start: 0.8262 (ptm) cc_final: 0.7984 (ptp) REVERT: P 162 TYR cc_start: 0.8076 (t80) cc_final: 0.7782 (t80) outliers start: 27 outliers final: 17 residues processed: 219 average time/residue: 0.3581 time to fit residues: 121.3411 Evaluate side-chains 206 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 131 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 260 optimal weight: 7.9990 chunk 198 optimal weight: 0.0010 chunk 136 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 280 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23679 Z= 0.178 Angle : 0.522 8.109 32017 Z= 0.257 Chirality : 0.042 0.179 3541 Planarity : 0.004 0.040 4122 Dihedral : 10.861 173.243 3238 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.40 % Allowed : 10.59 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.16), residues: 2899 helix: 1.67 (0.14), residues: 1428 sheet: -0.13 (0.24), residues: 433 loop : -0.79 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 130 HIS 0.006 0.001 HIS P 153 PHE 0.013 0.001 PHE A 46 TYR 0.018 0.001 TYR P 162 ARG 0.005 0.000 ARG P 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.5282 (pmm) cc_final: 0.4858 (pmm) REVERT: A 77 MET cc_start: 0.8247 (ppp) cc_final: 0.7945 (ppp) REVERT: A 684 MET cc_start: 0.5842 (ptm) cc_final: 0.5496 (ptm) REVERT: F 107 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: F 227 MET cc_start: 0.7905 (mmt) cc_final: 0.7602 (mmt) REVERT: C 143 TYR cc_start: 0.8521 (m-80) cc_final: 0.8313 (m-80) REVERT: D 47 MET cc_start: 0.7084 (tpt) cc_final: 0.6061 (ptp) REVERT: D 325 MET cc_start: 0.8164 (tpt) cc_final: 0.7806 (tpt) REVERT: O 127 MET cc_start: 0.7495 (ttm) cc_final: 0.6943 (tpt) REVERT: P 127 MET cc_start: 0.6718 (mtp) cc_final: 0.5807 (mmm) REVERT: P 162 TYR cc_start: 0.8062 (t80) cc_final: 0.7562 (t80) outliers start: 35 outliers final: 24 residues processed: 229 average time/residue: 0.3406 time to fit residues: 122.4013 Evaluate side-chains 215 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 190 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 61 SER Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 233 optimal weight: 1.9990 chunk 159 optimal weight: 0.0050 chunk 4 optimal weight: 20.0000 chunk 208 optimal weight: 4.9990 chunk 115 optimal weight: 0.2980 chunk 239 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 143 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN E 225 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23679 Z= 0.219 Angle : 0.538 8.872 32017 Z= 0.266 Chirality : 0.042 0.192 3541 Planarity : 0.004 0.040 4122 Dihedral : 10.281 167.923 3238 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.69 % Allowed : 11.20 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.16), residues: 2899 helix: 1.65 (0.14), residues: 1428 sheet: -0.09 (0.25), residues: 433 loop : -0.82 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 130 HIS 0.006 0.001 HIS P 153 PHE 0.014 0.001 PHE F 255 TYR 0.017 0.001 TYR P 162 ARG 0.011 0.000 ARG P 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.5401 (pmm) cc_final: 0.5007 (pmm) REVERT: A 77 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7885 (ppp) REVERT: F 107 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: C 132 MET cc_start: 0.8587 (ppp) cc_final: 0.8379 (ptm) REVERT: C 143 TYR cc_start: 0.8561 (m-80) cc_final: 0.8322 (m-80) REVERT: D 47 MET cc_start: 0.7234 (tpt) cc_final: 0.6060 (ptm) REVERT: D 325 MET cc_start: 0.8138 (tpt) cc_final: 0.7911 (tpt) REVERT: E 227 MET cc_start: 0.7962 (mmm) cc_final: 0.7659 (mmm) REVERT: O 127 MET cc_start: 0.7511 (ttm) cc_final: 0.6921 (tpt) REVERT: P 127 MET cc_start: 0.6688 (mtp) cc_final: 0.6351 (mmm) REVERT: P 162 TYR cc_start: 0.8073 (t80) cc_final: 0.7504 (t80) outliers start: 42 outliers final: 28 residues processed: 224 average time/residue: 0.3545 time to fit residues: 123.7519 Evaluate side-chains 213 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 94 optimal weight: 3.9990 chunk 252 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 280 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 129 optimal weight: 0.0370 chunk 23 optimal weight: 40.0000 chunk 92 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23679 Z= 0.202 Angle : 0.530 9.590 32017 Z= 0.261 Chirality : 0.042 0.253 3541 Planarity : 0.004 0.038 4122 Dihedral : 9.928 171.692 3238 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.65 % Allowed : 12.16 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.16), residues: 2899 helix: 1.64 (0.14), residues: 1428 sheet: -0.07 (0.25), residues: 433 loop : -0.79 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 130 HIS 0.005 0.001 HIS P 153 PHE 0.014 0.001 PHE A 621 TYR 0.017 0.001 TYR P 162 ARG 0.010 0.000 ARG P 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.5472 (pmm) cc_final: 0.5076 (pmm) REVERT: A 77 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7840 (ppp) REVERT: A 388 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7738 (mpp) REVERT: A 502 LYS cc_start: 0.8867 (mttp) cc_final: 0.8665 (mtmm) REVERT: A 554 ASP cc_start: 0.7470 (m-30) cc_final: 0.7233 (m-30) REVERT: F 107 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7168 (tt0) REVERT: B 176 MET cc_start: 0.7606 (mtt) cc_final: 0.7337 (mtt) REVERT: C 143 TYR cc_start: 0.8583 (m-80) cc_final: 0.8319 (m-80) REVERT: D 47 MET cc_start: 0.7285 (tpt) cc_final: 0.6088 (ptp) REVERT: O 127 MET cc_start: 0.7458 (ttm) cc_final: 0.6920 (tpt) REVERT: O 182 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8116 (ttp80) REVERT: P 121 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7026 (p0) REVERT: P 127 MET cc_start: 0.6618 (mtp) cc_final: 0.6278 (mmm) REVERT: P 162 TYR cc_start: 0.8117 (t80) cc_final: 0.7529 (t80) outliers start: 41 outliers final: 30 residues processed: 227 average time/residue: 0.3551 time to fit residues: 125.5492 Evaluate side-chains 222 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 187 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 121 ASP Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 270 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 204 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 236 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 279 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23679 Z= 0.175 Angle : 0.535 12.624 32017 Z= 0.261 Chirality : 0.042 0.210 3541 Planarity : 0.004 0.037 4122 Dihedral : 9.501 157.337 3238 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.69 % Allowed : 12.80 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.16), residues: 2899 helix: 1.67 (0.14), residues: 1428 sheet: -0.08 (0.25), residues: 435 loop : -0.75 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 130 HIS 0.006 0.001 HIS P 153 PHE 0.016 0.001 PHE A 621 TYR 0.016 0.001 TYR P 162 ARG 0.016 0.000 ARG P 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 196 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.5341 (pmm) cc_final: 0.4943 (pmm) REVERT: A 77 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7804 (ppp) REVERT: A 388 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7760 (mpp) REVERT: A 502 LYS cc_start: 0.8796 (mttp) cc_final: 0.8576 (mtmm) REVERT: A 554 ASP cc_start: 0.7410 (m-30) cc_final: 0.7174 (m-30) REVERT: F 107 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: C 143 TYR cc_start: 0.8567 (m-80) cc_final: 0.8291 (m-80) REVERT: D 47 MET cc_start: 0.7302 (tpt) cc_final: 0.6047 (ptp) REVERT: O 127 MET cc_start: 0.7458 (ttm) cc_final: 0.6959 (tpt) REVERT: O 182 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8210 (pmt-80) REVERT: P 111 GLN cc_start: 0.6883 (pp30) cc_final: 0.6682 (pp30) REVERT: P 121 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6915 (p0) REVERT: P 127 MET cc_start: 0.6560 (mtp) cc_final: 0.5680 (mmm) outliers start: 42 outliers final: 33 residues processed: 227 average time/residue: 0.3602 time to fit residues: 128.0777 Evaluate side-chains 228 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 121 ASP Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 172 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 219 optimal weight: 6.9990 chunk 254 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23679 Z= 0.189 Angle : 0.545 11.356 32017 Z= 0.268 Chirality : 0.042 0.216 3541 Planarity : 0.004 0.038 4122 Dihedral : 9.141 153.219 3238 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.77 % Allowed : 13.08 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2899 helix: 1.66 (0.14), residues: 1420 sheet: -0.07 (0.25), residues: 435 loop : -0.73 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 130 HIS 0.006 0.001 HIS P 153 PHE 0.016 0.001 PHE A 621 TYR 0.028 0.001 TYR P 162 ARG 0.015 0.000 ARG P 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 188 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.5444 (pmm) cc_final: 0.5121 (pmm) REVERT: A 77 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7798 (ppp) REVERT: A 388 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7699 (mpp) REVERT: A 502 LYS cc_start: 0.8800 (mttp) cc_final: 0.8579 (mtmm) REVERT: A 554 ASP cc_start: 0.7410 (m-30) cc_final: 0.7181 (m-30) REVERT: F 107 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: B 176 MET cc_start: 0.7582 (mtt) cc_final: 0.7198 (mtt) REVERT: D 47 MET cc_start: 0.7350 (tpt) cc_final: 0.6540 (tpt) REVERT: O 127 MET cc_start: 0.7470 (ttm) cc_final: 0.6950 (tpt) REVERT: O 182 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8185 (pmt-80) REVERT: P 121 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6647 (p0) REVERT: P 127 MET cc_start: 0.6612 (mtp) cc_final: 0.6326 (mmm) REVERT: P 162 TYR cc_start: 0.8057 (t80) cc_final: 0.7608 (t80) outliers start: 44 outliers final: 34 residues processed: 220 average time/residue: 0.3593 time to fit residues: 123.3702 Evaluate side-chains 223 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 121 ASP Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 267 optimal weight: 20.0000 chunk 244 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 156 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 204 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 259 optimal weight: 9.9990 chunk 171 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23679 Z= 0.148 Angle : 0.529 12.119 32017 Z= 0.257 Chirality : 0.041 0.211 3541 Planarity : 0.003 0.045 4122 Dihedral : 8.541 147.151 3238 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.65 % Allowed : 13.24 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2899 helix: 1.70 (0.14), residues: 1422 sheet: -0.02 (0.25), residues: 435 loop : -0.66 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 130 HIS 0.007 0.001 HIS P 153 PHE 0.015 0.001 PHE A 621 TYR 0.026 0.001 TYR P 162 ARG 0.015 0.000 ARG P 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.5326 (pmm) cc_final: 0.4995 (pmm) REVERT: A 77 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7774 (ppp) REVERT: A 388 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7589 (mpp) REVERT: A 554 ASP cc_start: 0.7389 (m-30) cc_final: 0.7173 (m-30) REVERT: F 107 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: D 47 MET cc_start: 0.7340 (tpt) cc_final: 0.6606 (tpt) REVERT: E 223 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: O 127 MET cc_start: 0.7473 (ttm) cc_final: 0.6950 (tpt) REVERT: O 182 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8180 (pmt-80) REVERT: P 121 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6568 (p0) REVERT: P 127 MET cc_start: 0.6593 (mtp) cc_final: 0.6350 (mmm) REVERT: P 162 TYR cc_start: 0.8081 (t80) cc_final: 0.7515 (t80) outliers start: 41 outliers final: 29 residues processed: 219 average time/residue: 0.3610 time to fit residues: 124.2346 Evaluate side-chains 218 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 121 ASP Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 275 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 288 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 177 optimal weight: 0.0970 chunk 141 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 23679 Z= 0.485 Angle : 0.677 12.355 32017 Z= 0.340 Chirality : 0.048 0.206 3541 Planarity : 0.005 0.057 4122 Dihedral : 9.066 151.117 3238 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.48 % Allowed : 13.40 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.16), residues: 2899 helix: 1.42 (0.14), residues: 1385 sheet: -0.27 (0.25), residues: 431 loop : -0.96 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 130 HIS 0.009 0.002 HIS D 73 PHE 0.020 0.002 PHE F 255 TYR 0.027 0.002 TYR P 162 ARG 0.014 0.001 ARG P 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5798 Ramachandran restraints generated. 2899 Oldfield, 0 Emsley, 2899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 178 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.5665 (pmm) cc_final: 0.5337 (pmm) REVERT: A 77 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7633 (ppp) REVERT: A 388 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7752 (mpp) REVERT: A 502 LYS cc_start: 0.8754 (mtmm) cc_final: 0.8544 (mtmm) REVERT: A 554 ASP cc_start: 0.7575 (m-30) cc_final: 0.7350 (m-30) REVERT: F 107 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: F 375 PHE cc_start: 0.6935 (t80) cc_final: 0.6662 (t80) REVERT: C 227 MET cc_start: 0.8059 (mmm) cc_final: 0.7842 (mmt) REVERT: D 47 MET cc_start: 0.7406 (tpt) cc_final: 0.6847 (tpt) REVERT: D 107 GLU cc_start: 0.7599 (pt0) cc_final: 0.7321 (pt0) REVERT: E 72 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7392 (mm-30) REVERT: O 127 MET cc_start: 0.7497 (ttm) cc_final: 0.7001 (tpt) REVERT: P 93 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7478 (pp30) REVERT: P 121 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6631 (p0) REVERT: P 127 MET cc_start: 0.6505 (mtp) cc_final: 0.5693 (mmt) outliers start: 37 outliers final: 25 residues processed: 207 average time/residue: 0.3448 time to fit residues: 112.8521 Evaluate side-chains 205 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 176 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 121 ASP Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain P residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 245 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 212 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 230 optimal weight: 0.0000 chunk 96 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 202 optimal weight: 0.3980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.122088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.080780 restraints weight = 41209.098| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.21 r_work: 0.2993 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23679 Z= 0.167 Angle : 0.555 12.076 32017 Z= 0.272 Chirality : 0.042 0.201 3541 Planarity : 0.004 0.052 4122 Dihedral : 8.448 147.386 3238 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.32 % Allowed : 13.76 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2899 helix: 1.53 (0.14), residues: 1416 sheet: -0.13 (0.25), residues: 429 loop : -0.87 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 130 HIS 0.007 0.001 HIS P 153 PHE 0.015 0.001 PHE A 621 TYR 0.038 0.001 TYR P 162 ARG 0.014 0.000 ARG P 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4501.82 seconds wall clock time: 82 minutes 48.76 seconds (4968.76 seconds total)