Starting phenix.real_space_refine on Mon Feb 19 00:26:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enc_28270/02_2024/8enc_28270_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enc_28270/02_2024/8enc_28270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enc_28270/02_2024/8enc_28270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enc_28270/02_2024/8enc_28270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enc_28270/02_2024/8enc_28270_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8enc_28270/02_2024/8enc_28270_updated.pdb" } resolution = 3.6 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= 0.002 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 10 5.49 5 Mg 5 5.21 5 S 138 5.16 5 C 14642 2.51 5 N 3940 2.21 5 O 4485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 507": "OE1" <-> "OE2" Residue "M TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "O GLU 104": "OE1" <-> "OE2" Residue "O GLU 122": "OE1" <-> "OE2" Residue "P TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 150": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23220 Number of models: 1 Model: "" Number of chains: 13 Chain: "M" Number of atoms: 5938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5938 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 28, 'TRANS': 713} Chain breaks: 3 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: "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: "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: "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} 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} Time building chain proxies: 11.98, per 1000 atoms: 0.52 Number of scatterers: 23220 At special positions: 0 Unit cell: (159.544, 108.878, 247.94, 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 10 15.00 Mg 5 11.99 O 4485 8.00 N 3940 7.00 C 14642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.20 Conformation dependent library (CDL) restraints added in 4.0 seconds 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 30 sheets defined 50.7% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'M' and resid 7 through 16 removed outlier: 6.480A pdb=" N ALA M 11 " --> pdb=" O VAL M 8 " (cutoff:3.500A) Proline residue: M 14 - end of helix Processing helix chain 'M' and resid 20 through 27 Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing helix chain 'M' and resid 82 through 84 No H-bonds generated for 'chain 'M' and resid 82 through 84' Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 98 through 110 removed outlier: 4.007A pdb=" N LEU M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 134 No H-bonds generated for 'chain 'M' and resid 132 through 134' Processing helix chain 'M' and resid 136 through 142 Processing helix chain 'M' and resid 154 through 167 Processing helix chain 'M' and resid 184 through 198 Processing helix chain 'M' and resid 217 through 230 Proline residue: M 225 - end of helix Processing helix chain 'M' and resid 271 through 274 No H-bonds generated for 'chain 'M' and resid 271 through 274' Processing helix chain 'M' and resid 284 through 289 Processing helix chain 'M' and resid 295 through 300 Processing helix chain 'M' and resid 311 through 314 No H-bonds generated for 'chain 'M' and resid 311 through 314' Processing helix chain 'M' and resid 325 through 337 Processing helix chain 'M' and resid 343 through 361 removed outlier: 3.576A pdb=" N PHE M 359 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY M 360 " --> pdb=" O ILE M 356 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASN M 361 " --> pdb=" O MET M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 388 Processing helix chain 'M' and resid 392 through 400 Processing helix chain 'M' and resid 417 through 447 Processing helix chain 'M' and resid 473 through 504 Processing helix chain 'M' and resid 515 through 523 removed outlier: 4.822A pdb=" N CYS M 520 " --> pdb=" O ASP M 516 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE M 521 " --> pdb=" O LEU M 517 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU M 523 " --> pdb=" O ALA M 519 " (cutoff:3.500A) Processing helix chain 'M' and resid 530 through 539 removed outlier: 3.642A pdb=" N MET M 539 " --> pdb=" O GLU M 535 " (cutoff:3.500A) Processing helix chain 'M' and resid 545 through 556 Processing helix chain 'M' and resid 593 through 597 Processing helix chain 'M' and resid 603 through 610 Processing helix chain 'M' and resid 615 through 619 Processing helix chain 'M' and resid 647 through 664 removed outlier: 3.983A pdb=" N ASN M 661 " --> pdb=" O LYS M 657 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER M 664 " --> pdb=" O THR M 660 " (cutoff:3.500A) Processing helix chain 'M' and resid 686 through 696 Processing helix chain 'M' and resid 698 through 706 Processing helix chain 'M' and resid 715 through 726 removed outlier: 6.037A pdb=" N ILE M 724 " --> pdb=" O GLN M 720 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU M 725 " --> pdb=" O ARG M 721 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN M 726 " --> pdb=" O TYR M 722 " (cutoff:3.500A) Processing helix chain 'M' and resid 739 through 749 removed outlier: 3.695A pdb=" N LEU M 749 " --> pdb=" O LEU M 745 " (cutoff:3.500A) Processing helix chain 'M' and resid 753 through 755 No H-bonds generated for 'chain 'M' and resid 753 through 755' Processing helix chain 'M' and resid 767 through 780 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' 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 145 removed outlier: 3.631A 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: 3.823A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.857A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.940A 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: 3.696A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.560A 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 302 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: 3.750A 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 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 80 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 195 removed outlier: 3.889A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.968A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.527A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.788A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 351 through 354 removed outlier: 4.080A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.753A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) 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 145 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: 3.772A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.959A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.789A 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 256 removed outlier: 3.508A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.674A 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 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 338 through 348 Processing helix chain 'D' and resid 351 through 354 Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 367 through 371 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 145 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 196 removed outlier: 3.610A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.807A pdb=" N LEU E 216 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.508A pdb=" N PHE E 255 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 removed outlier: 3.816A 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 351 through 355 removed outlier: 3.586A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 371 removed outlier: 4.072A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' 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: 4.042A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 232 removed outlier: 3.598A pdb=" N SER F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 removed outlier: 3.598A pdb=" N ARG F 256 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 274 through 284 removed outlier: 3.529A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 296 removed outlier: 3.714A pdb=" N ARG F 290 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS F 291 " --> pdb=" O ASP F 288 " (cutoff:3.500A) 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 351 through 354 removed outlier: 4.002A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 367 through 371 removed outlier: 3.682A pdb=" N VAL F 370 " --> pdb=" O PRO F 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 209 removed outlier: 4.658A pdb=" N GLN O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 209 removed outlier: 3.556A pdb=" N ARG P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA P 209 " --> pdb=" O LYS P 205 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'M' and resid 49 through 51 Processing sheet with id= B, first strand: chain 'M' and resid 115 through 118 removed outlier: 10.385A pdb=" N CYS M 122 " --> pdb=" O PRO M 667 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE M 669 " --> pdb=" O CYS M 122 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR M 124 " --> pdb=" O PHE M 669 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG M 671 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN M 172 " --> pdb=" O PHE M 456 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE M 462 " --> pdb=" O ILE M 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER M 260 " --> pdb=" O HIS M 251 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 364 through 366 Processing sheet with id= D, first strand: chain 'M' and resid 403 through 406 Processing sheet with id= E, first strand: chain 'M' and resid 563 through 565 removed outlier: 3.598A pdb=" N PHE M 577 " --> pdb=" O TYR M 588 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'M' and resid 711 through 714 removed outlier: 3.805A pdb=" N ASN M 711 " --> pdb=" O PHE M 765 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.564A pdb=" N GLY B 20 " --> pdb=" O VAL B 9 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= I, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= J, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.381A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 238 through 240 Processing sheet with id= L, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= M, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= N, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= O, first strand: chain 'C' and resid 298 through 300 Processing sheet with id= P, first strand: chain 'C' and resid 238 through 240 Processing sheet with id= Q, first strand: chain 'D' and resid 8 through 11 Processing sheet with id= R, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'D' and resid 103 through 107 Processing sheet with id= T, first strand: chain 'D' and resid 298 through 300 Processing sheet with id= U, first strand: chain 'D' and resid 238 through 240 Processing sheet with id= V, first strand: chain 'E' and resid 8 through 11 Processing sheet with id= W, first strand: chain 'E' and resid 35 through 38 removed outlier: 3.615A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 103 through 107 Processing sheet with id= Y, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.217A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 238 through 240 Processing sheet with id= AA, first strand: chain 'F' and resid 132 through 136 removed outlier: 6.458A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.633A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.275A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 238 through 240 1111 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: 9.02 Time building geometry restraints manager: 9.89 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: 7504 1.34 - 1.46: 3004 1.46 - 1.57: 12907 1.57 - 1.69: 15 1.69 - 1.81: 241 Bond restraints: 23671 Sorted by residual: bond pdb=" N LYS M 640 " pdb=" CA LYS M 640 " ideal model delta sigma weight residual 1.456 1.476 -0.019 1.21e-02 6.83e+03 2.56e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.55e+00 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.39e+00 ... (remaining 23666 not shown) Histogram of bond angle deviations from ideal: 95.43 - 103.62: 329 103.62 - 111.81: 11213 111.81 - 120.00: 10130 120.00 - 128.19: 10130 128.19 - 136.38: 196 Bond angle restraints: 31998 Sorted by residual: angle pdb=" CA ARG O 105 " pdb=" CB ARG O 105 " pdb=" CG ARG O 105 " ideal model delta sigma weight residual 114.10 122.43 -8.33 2.00e+00 2.50e-01 1.74e+01 angle pdb=" C LEU P 110 " pdb=" N GLN P 111 " pdb=" CA GLN P 111 " ideal model delta sigma weight residual 120.29 114.60 5.69 1.42e+00 4.96e-01 1.61e+01 angle pdb=" N GLN P 111 " pdb=" CA GLN P 111 " pdb=" CB GLN P 111 " ideal model delta sigma weight residual 110.16 115.87 -5.71 1.48e+00 4.57e-01 1.49e+01 angle pdb=" C GLU O 104 " pdb=" N ARG O 105 " pdb=" CA ARG O 105 " ideal model delta sigma weight residual 121.58 114.11 7.47 1.95e+00 2.63e-01 1.47e+01 angle pdb=" N LYS M 640 " pdb=" CA LYS M 640 " pdb=" C LYS M 640 " ideal model delta sigma weight residual 109.07 115.10 -6.03 1.61e+00 3.86e-01 1.40e+01 ... (remaining 31993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 13574 23.62 - 47.24: 695 47.24 - 70.86: 94 70.86 - 94.48: 26 94.48 - 118.10: 3 Dihedral angle restraints: 14392 sinusoidal: 5899 harmonic: 8493 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.11 118.10 1 2.00e+01 2.50e-03 3.53e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -174.39 114.39 1 2.00e+01 2.50e-03 3.39e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -168.86 108.86 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 14389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2640 0.037 - 0.074: 597 0.074 - 0.111: 234 0.111 - 0.148: 63 0.148 - 0.186: 2 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CA ARG O 105 " pdb=" N ARG O 105 " pdb=" C ARG O 105 " pdb=" CB ARG O 105 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CA ILE M 174 " pdb=" N ILE M 174 " pdb=" C ILE M 174 " pdb=" CB ILE M 174 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE M 585 " pdb=" N ILE M 585 " pdb=" C ILE M 585 " pdb=" CB ILE M 585 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 3533 not shown) Planarity restraints: 4125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN M 80 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO M 81 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO M 81 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO M 81 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 182 " 0.031 9.50e-02 1.11e+02 1.89e-02 2.14e+00 pdb=" NE ARG P 182 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG P 182 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG P 182 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG P 182 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG O 105 " 0.007 2.00e-02 2.50e+03 1.41e-02 2.00e+00 pdb=" C ARG O 105 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG O 105 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU O 106 " 0.008 2.00e-02 2.50e+03 ... (remaining 4122 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 100 2.48 - 3.08: 16748 3.08 - 3.69: 35208 3.69 - 4.29: 49776 4.29 - 4.90: 84321 Nonbonded interactions: 186153 Sorted by model distance: nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.869 2.170 nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 1.990 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 2.004 2.170 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.080 2.440 nonbonded pdb=" O CYS M 538 " pdb=" NZ LYS M 598 " model vdw 2.119 2.520 ... (remaining 186148 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.790 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: 25.200 Check model and map are aligned: 0.390 Set scattering table: 0.210 Process input model: 62.520 Find NCS groups from input model: 1.440 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: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23671 Z= 0.163 Angle : 0.566 8.794 31998 Z= 0.305 Chirality : 0.039 0.186 3536 Planarity : 0.003 0.037 4125 Dihedral : 14.184 118.104 8932 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 0.08 % Allowed : 0.28 % 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: 1.79 (0.17), residues: 2907 helix: 2.16 (0.15), residues: 1357 sheet: 0.22 (0.25), residues: 414 loop : 0.49 (0.20), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 340 HIS 0.010 0.001 HIS P 153 PHE 0.015 0.001 PHE E 223 TYR 0.020 0.001 TYR B 279 ARG 0.025 0.001 ARG P 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 206 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8355 (ptp) cc_final: 0.8097 (pmm) REVERT: M 165 MET cc_start: 0.9242 (tmm) cc_final: 0.8845 (tmm) REVERT: M 362 MET cc_start: 0.8776 (mmm) cc_final: 0.8526 (mmm) REVERT: M 493 MET cc_start: 0.8839 (ttp) cc_final: 0.8458 (ppp) REVERT: M 585 ILE cc_start: 0.9564 (mt) cc_final: 0.9183 (tp) REVERT: M 690 MET cc_start: 0.9180 (mmm) cc_final: 0.8579 (mmm) REVERT: M 693 LEU cc_start: 0.9190 (tt) cc_final: 0.8912 (pp) REVERT: M 765 PHE cc_start: 0.8706 (m-80) cc_final: 0.8375 (m-10) REVERT: B 82 MET cc_start: 0.8986 (tpt) cc_final: 0.8607 (tpt) REVERT: C 374 CYS cc_start: 0.6436 (p) cc_final: 0.5832 (m) REVERT: E 283 MET cc_start: 0.9015 (mmt) cc_final: 0.8759 (mmt) REVERT: F 227 MET cc_start: 0.8972 (mmm) cc_final: 0.8710 (tpp) REVERT: O 105 ARG cc_start: 0.9103 (pmt170) cc_final: 0.8526 (pmt170) REVERT: O 178 ARG cc_start: 0.8793 (pmt-80) cc_final: 0.8552 (pmt-80) REVERT: P 127 MET cc_start: 0.9150 (ptp) cc_final: 0.8947 (mmt) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.4092 time to fit residues: 126.8670 Evaluate side-chains 158 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 264 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 104 ASN ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23671 Z= 0.186 Angle : 0.544 7.930 31998 Z= 0.270 Chirality : 0.042 0.154 3536 Planarity : 0.003 0.038 4125 Dihedral : 5.204 97.490 3235 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 0.40 % Allowed : 5.10 % Favored : 94.50 % 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: 1.67 (0.16), residues: 2907 helix: 2.06 (0.15), residues: 1356 sheet: 0.18 (0.25), residues: 419 loop : 0.44 (0.20), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 79 HIS 0.012 0.001 HIS O 153 PHE 0.021 0.001 PHE M 488 TYR 0.017 0.001 TYR B 279 ARG 0.014 0.000 ARG P 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8399 (ptp) cc_final: 0.8153 (pmm) REVERT: M 165 MET cc_start: 0.9298 (tmm) cc_final: 0.8851 (tmm) REVERT: M 493 MET cc_start: 0.8864 (ttp) cc_final: 0.8367 (tmm) REVERT: M 585 ILE cc_start: 0.9549 (mt) cc_final: 0.9144 (tp) REVERT: M 693 LEU cc_start: 0.9179 (tt) cc_final: 0.8970 (pp) REVERT: C 374 CYS cc_start: 0.6410 (p) cc_final: 0.6003 (m) REVERT: F 227 MET cc_start: 0.9061 (mmm) cc_final: 0.8778 (tpp) REVERT: P 153 HIS cc_start: 0.8769 (m-70) cc_final: 0.8474 (m90) outliers start: 10 outliers final: 4 residues processed: 173 average time/residue: 0.4180 time to fit residues: 108.3595 Evaluate side-chains 157 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 179 optimal weight: 0.0670 chunk 72 optimal weight: 0.2980 chunk 264 optimal weight: 0.8980 chunk 285 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23671 Z= 0.125 Angle : 0.512 8.255 31998 Z= 0.252 Chirality : 0.040 0.150 3536 Planarity : 0.003 0.054 4125 Dihedral : 4.882 82.110 3235 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.72 % Favored : 97.25 % Rotamer: Outliers : 0.64 % Allowed : 7.03 % Favored : 92.33 % 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: 1.79 (0.16), residues: 2907 helix: 2.11 (0.15), residues: 1351 sheet: 0.49 (0.25), residues: 429 loop : 0.45 (0.20), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 79 HIS 0.012 0.001 HIS O 153 PHE 0.013 0.001 PHE M 488 TYR 0.012 0.001 TYR B 279 ARG 0.008 0.000 ARG P 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8584 (ptp) cc_final: 0.8314 (pmm) REVERT: M 165 MET cc_start: 0.9314 (tmm) cc_final: 0.8824 (tmm) REVERT: M 330 MET cc_start: 0.9240 (mmm) cc_final: 0.9021 (mmt) REVERT: M 357 MET cc_start: 0.8508 (tmm) cc_final: 0.7921 (tpt) REVERT: M 493 MET cc_start: 0.8955 (ttp) cc_final: 0.8390 (tmm) REVERT: M 740 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8314 (pptt) REVERT: B 283 MET cc_start: 0.8656 (mmm) cc_final: 0.8357 (mmm) REVERT: C 374 CYS cc_start: 0.6493 (p) cc_final: 0.6002 (m) REVERT: F 227 MET cc_start: 0.9069 (mmm) cc_final: 0.8751 (tpp) REVERT: O 127 MET cc_start: 0.8680 (ppp) cc_final: 0.8395 (ppp) outliers start: 16 outliers final: 7 residues processed: 175 average time/residue: 0.4142 time to fit residues: 109.1860 Evaluate side-chains 161 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 251 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN D 162 ASN F 371 HIS ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 153 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23671 Z= 0.278 Angle : 0.573 8.762 31998 Z= 0.281 Chirality : 0.042 0.161 3536 Planarity : 0.003 0.036 4125 Dihedral : 4.835 69.524 3235 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 0.84 % Allowed : 9.24 % Favored : 89.92 % 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: 1.73 (0.16), residues: 2907 helix: 2.07 (0.15), residues: 1345 sheet: 0.29 (0.26), residues: 414 loop : 0.49 (0.20), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 79 HIS 0.011 0.001 HIS P 153 PHE 0.012 0.001 PHE F 255 TYR 0.016 0.001 TYR M 142 ARG 0.009 0.001 ARG M 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8731 (ptp) cc_final: 0.8319 (pmm) REVERT: M 90 MET cc_start: 0.8601 (mmm) cc_final: 0.8190 (mmp) REVERT: M 165 MET cc_start: 0.9313 (tmm) cc_final: 0.8826 (tmm) REVERT: M 357 MET cc_start: 0.8577 (tmm) cc_final: 0.8082 (tpt) REVERT: M 493 MET cc_start: 0.8959 (ttp) cc_final: 0.8424 (tmm) REVERT: M 593 TRP cc_start: 0.8590 (m-10) cc_final: 0.8262 (m-10) REVERT: M 740 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8390 (pptt) REVERT: C 374 CYS cc_start: 0.6230 (p) cc_final: 0.5383 (m) outliers start: 21 outliers final: 11 residues processed: 170 average time/residue: 0.4044 time to fit residues: 104.4452 Evaluate side-chains 161 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 530 ILE Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 202 ASN Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 209 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 143 optimal weight: 6.9990 chunk 252 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23671 Z= 0.163 Angle : 0.519 9.046 31998 Z= 0.255 Chirality : 0.040 0.168 3536 Planarity : 0.003 0.046 4125 Dihedral : 4.685 67.782 3235 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 1.00 % Allowed : 10.25 % Favored : 88.75 % 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: 1.81 (0.16), residues: 2907 helix: 2.10 (0.15), residues: 1351 sheet: 0.42 (0.25), residues: 443 loop : 0.53 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 79 HIS 0.026 0.001 HIS P 153 PHE 0.015 0.001 PHE E 31 TYR 0.023 0.001 TYR P 162 ARG 0.009 0.000 ARG P 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8711 (ptp) cc_final: 0.8352 (pmm) REVERT: M 90 MET cc_start: 0.8688 (mmm) cc_final: 0.8338 (mmp) REVERT: M 165 MET cc_start: 0.9301 (tmm) cc_final: 0.8854 (tmm) REVERT: M 330 MET cc_start: 0.9322 (mmm) cc_final: 0.9110 (mmt) REVERT: M 493 MET cc_start: 0.8969 (ttp) cc_final: 0.8428 (tmm) REVERT: M 740 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8399 (pptt) REVERT: C 374 CYS cc_start: 0.6601 (p) cc_final: 0.6226 (m) REVERT: E 223 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: O 127 MET cc_start: 0.8418 (ppp) cc_final: 0.8136 (ppp) outliers start: 25 outliers final: 11 residues processed: 172 average time/residue: 0.4134 time to fit residues: 108.1333 Evaluate side-chains 163 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 4.9990 chunk 253 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 238 ASN ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23671 Z= 0.228 Angle : 0.552 11.592 31998 Z= 0.270 Chirality : 0.041 0.185 3536 Planarity : 0.003 0.039 4125 Dihedral : 4.704 65.325 3235 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.73 % Rotamer: Outliers : 0.84 % Allowed : 10.89 % Favored : 88.27 % 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: 1.78 (0.16), residues: 2907 helix: 2.06 (0.15), residues: 1356 sheet: 0.33 (0.26), residues: 418 loop : 0.57 (0.20), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 79 HIS 0.008 0.001 HIS O 153 PHE 0.020 0.001 PHE M 247 TYR 0.014 0.001 TYR M 142 ARG 0.017 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8774 (ptp) cc_final: 0.8400 (pmm) REVERT: M 90 MET cc_start: 0.8709 (mmm) cc_final: 0.8373 (mmp) REVERT: M 165 MET cc_start: 0.9291 (tmm) cc_final: 0.8825 (tmm) REVERT: M 357 MET cc_start: 0.8557 (tmm) cc_final: 0.8122 (tpp) REVERT: M 493 MET cc_start: 0.8955 (ttp) cc_final: 0.8454 (tmm) REVERT: M 593 TRP cc_start: 0.8599 (m-10) cc_final: 0.8275 (m-10) REVERT: M 740 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8335 (pptt) REVERT: B 190 MET cc_start: 0.8765 (mtt) cc_final: 0.8539 (mtt) REVERT: C 374 CYS cc_start: 0.6559 (p) cc_final: 0.5978 (m) REVERT: E 47 MET cc_start: 0.8046 (tpp) cc_final: 0.7595 (tpp) REVERT: E 223 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8449 (m-80) outliers start: 21 outliers final: 16 residues processed: 169 average time/residue: 0.4439 time to fit residues: 113.2669 Evaluate side-chains 168 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 406 VAL Chi-restraints excluded: chain M residue 530 ILE Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 160 optimal weight: 0.4980 chunk 205 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 280 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23671 Z= 0.167 Angle : 0.538 10.426 31998 Z= 0.263 Chirality : 0.040 0.160 3536 Planarity : 0.003 0.049 4125 Dihedral : 4.633 65.665 3235 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.14 % Rotamer: Outliers : 0.84 % Allowed : 11.41 % Favored : 87.75 % 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: 1.79 (0.16), residues: 2907 helix: 2.05 (0.15), residues: 1351 sheet: 0.40 (0.25), residues: 443 loop : 0.57 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 79 HIS 0.008 0.001 HIS O 153 PHE 0.013 0.001 PHE M 488 TYR 0.016 0.001 TYR P 162 ARG 0.010 0.000 ARG P 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8759 (ptp) cc_final: 0.8421 (pmm) REVERT: M 90 MET cc_start: 0.8688 (mmm) cc_final: 0.8346 (mmp) REVERT: M 165 MET cc_start: 0.9280 (tmm) cc_final: 0.8805 (tmm) REVERT: M 357 MET cc_start: 0.8547 (tmm) cc_final: 0.8071 (tpp) REVERT: M 493 MET cc_start: 0.8934 (ttp) cc_final: 0.8421 (tmm) REVERT: M 593 TRP cc_start: 0.8597 (m-10) cc_final: 0.8231 (m-10) REVERT: M 740 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8315 (pptt) REVERT: B 190 MET cc_start: 0.8735 (mtt) cc_final: 0.8482 (mtt) REVERT: C 374 CYS cc_start: 0.6597 (p) cc_final: 0.6007 (m) REVERT: E 47 MET cc_start: 0.8030 (tpp) cc_final: 0.7634 (tpp) REVERT: E 223 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8385 (m-80) REVERT: O 127 MET cc_start: 0.8370 (ppp) cc_final: 0.8124 (ppp) outliers start: 21 outliers final: 14 residues processed: 169 average time/residue: 0.4383 time to fit residues: 110.8569 Evaluate side-chains 166 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 220 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23671 Z= 0.148 Angle : 0.537 11.083 31998 Z= 0.261 Chirality : 0.040 0.151 3536 Planarity : 0.003 0.041 4125 Dihedral : 4.535 63.952 3235 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 0.80 % Allowed : 11.73 % Favored : 87.46 % 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: 1.79 (0.16), residues: 2907 helix: 2.05 (0.15), residues: 1356 sheet: 0.38 (0.26), residues: 418 loop : 0.59 (0.20), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 79 HIS 0.007 0.001 HIS P 153 PHE 0.014 0.001 PHE C 223 TYR 0.012 0.001 TYR M 142 ARG 0.010 0.000 ARG P 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8736 (ptp) cc_final: 0.8426 (pmm) REVERT: M 90 MET cc_start: 0.8652 (mmm) cc_final: 0.8313 (mmp) REVERT: M 165 MET cc_start: 0.9283 (tmm) cc_final: 0.8796 (tmm) REVERT: M 493 MET cc_start: 0.8995 (ttp) cc_final: 0.8441 (tmm) REVERT: M 593 TRP cc_start: 0.8591 (m-10) cc_final: 0.8175 (m-10) REVERT: M 740 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8327 (pptt) REVERT: B 190 MET cc_start: 0.8760 (mtt) cc_final: 0.8531 (mtt) REVERT: C 374 CYS cc_start: 0.6619 (p) cc_final: 0.6254 (m) REVERT: E 47 MET cc_start: 0.8010 (tpp) cc_final: 0.7655 (tpp) REVERT: E 223 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8305 (m-80) REVERT: O 141 MET cc_start: 0.8183 (mmt) cc_final: 0.7978 (mpp) REVERT: P 202 ASN cc_start: 0.9284 (m-40) cc_final: 0.8888 (p0) outliers start: 20 outliers final: 16 residues processed: 172 average time/residue: 0.4072 time to fit residues: 105.4128 Evaluate side-chains 167 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 0.7980 chunk 268 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 157 optimal weight: 0.4980 chunk 113 optimal weight: 0.3980 chunk 205 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 chunk 260 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 172 GLN ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23671 Z= 0.132 Angle : 0.543 11.642 31998 Z= 0.263 Chirality : 0.040 0.165 3536 Planarity : 0.003 0.056 4125 Dihedral : 4.477 62.596 3235 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 0.76 % Allowed : 12.09 % Favored : 87.14 % 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: 1.81 (0.16), residues: 2907 helix: 2.06 (0.15), residues: 1356 sheet: 0.46 (0.25), residues: 443 loop : 0.58 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 79 HIS 0.008 0.001 HIS P 153 PHE 0.012 0.001 PHE M 488 TYR 0.027 0.001 TYR P 162 ARG 0.014 0.000 ARG O 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8743 (ptp) cc_final: 0.8443 (pmm) REVERT: M 90 MET cc_start: 0.8646 (mmm) cc_final: 0.8303 (mmp) REVERT: M 165 MET cc_start: 0.9283 (tmm) cc_final: 0.8791 (tmm) REVERT: M 357 MET cc_start: 0.8356 (tmm) cc_final: 0.8135 (tmm) REVERT: M 493 MET cc_start: 0.9012 (ttp) cc_final: 0.8422 (tmm) REVERT: M 593 TRP cc_start: 0.8582 (m-10) cc_final: 0.8171 (m-10) REVERT: M 740 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8329 (pptt) REVERT: B 190 MET cc_start: 0.8743 (mtt) cc_final: 0.8502 (mtt) REVERT: C 374 CYS cc_start: 0.6507 (p) cc_final: 0.5903 (m) REVERT: E 47 MET cc_start: 0.7997 (tpp) cc_final: 0.7670 (tpp) REVERT: E 223 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8287 (m-80) REVERT: O 127 MET cc_start: 0.8401 (ppp) cc_final: 0.8071 (ppp) outliers start: 19 outliers final: 17 residues processed: 166 average time/residue: 0.4409 time to fit residues: 111.0815 Evaluate side-chains 166 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 178 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 686 ASN ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23671 Z= 0.195 Angle : 0.574 12.075 31998 Z= 0.278 Chirality : 0.041 0.170 3536 Planarity : 0.003 0.049 4125 Dihedral : 4.517 64.237 3235 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.97 % Rotamer: Outliers : 0.80 % Allowed : 12.21 % Favored : 86.98 % 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: 1.79 (0.16), residues: 2907 helix: 2.03 (0.15), residues: 1361 sheet: 0.38 (0.26), residues: 418 loop : 0.61 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 79 HIS 0.009 0.001 HIS P 153 PHE 0.012 0.001 PHE F 255 TYR 0.023 0.001 TYR P 162 ARG 0.019 0.001 ARG P 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5814 Ramachandran restraints generated. 2907 Oldfield, 0 Emsley, 2907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 77 MET cc_start: 0.8759 (ptp) cc_final: 0.8417 (pmm) REVERT: M 90 MET cc_start: 0.8689 (mmm) cc_final: 0.8378 (mmp) REVERT: M 165 MET cc_start: 0.9265 (tmm) cc_final: 0.8765 (tmm) REVERT: M 357 MET cc_start: 0.8453 (tmm) cc_final: 0.8197 (tmm) REVERT: M 493 MET cc_start: 0.9003 (ttp) cc_final: 0.8450 (tmm) REVERT: M 593 TRP cc_start: 0.8666 (m-10) cc_final: 0.8226 (m-10) REVERT: M 740 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8348 (pptt) REVERT: B 190 MET cc_start: 0.8746 (mtt) cc_final: 0.8504 (mtt) REVERT: C 374 CYS cc_start: 0.6565 (p) cc_final: 0.5952 (m) REVERT: E 47 MET cc_start: 0.8088 (tpp) cc_final: 0.7789 (tpp) REVERT: E 223 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: O 127 MET cc_start: 0.8355 (ppp) cc_final: 0.8142 (ppp) REVERT: O 141 MET cc_start: 0.8430 (mmt) cc_final: 0.7944 (mpp) outliers start: 20 outliers final: 18 residues processed: 165 average time/residue: 0.4210 time to fit residues: 104.1802 Evaluate side-chains 169 residues out of total 2489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 684 MET Chi-restraints excluded: chain M residue 740 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 223 PHE Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain O residue 162 TYR Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 111 GLN Chi-restraints excluded: chain P residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 70 optimal weight: 30.0000 chunk 212 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.063472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.039970 restraints weight = 99427.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.041329 restraints weight = 43467.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.042194 restraints weight = 25355.568| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23671 Z= 0.206 Angle : 0.576 11.953 31998 Z= 0.281 Chirality : 0.041 0.162 3536 Planarity : 0.003 0.049 4125 Dihedral : 4.557 67.596 3235 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.72 % Favored : 97.25 % Rotamer: Outliers : 0.96 % Allowed : 12.21 % Favored : 86.82 % 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: 1.80 (0.16), residues: 2907 helix: 2.03 (0.15), residues: 1371 sheet: 0.35 (0.26), residues: 418 loop : 0.61 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 79 HIS 0.009 0.001 HIS P 153 PHE 0.012 0.001 PHE F 255 TYR 0.014 0.001 TYR M 142 ARG 0.014 0.001 ARG P 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4066.22 seconds wall clock time: 76 minutes 54.53 seconds (4614.53 seconds total)