Starting phenix.real_space_refine (version: dev) on Tue Feb 21 03:48:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2j_20572/02_2023/6q2j_20572_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2j_20572/02_2023/6q2j_20572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2j_20572/02_2023/6q2j_20572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2j_20572/02_2023/6q2j_20572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2j_20572/02_2023/6q2j_20572_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2j_20572/02_2023/6q2j_20572_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Process input model Symmetric amino acids flipped Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 294": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D ARG 294": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13796 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 98} Chain: "C" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1477 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 183} Chain: "E" Number of atoms: 4493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4493 Classifications: {'peptide': 571} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 535} Chain breaks: 5 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 98} Chain: "D" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1477 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 183} Chain: "F" Number of atoms: 4493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4493 Classifications: {'peptide': 571} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 535} Chain breaks: 5 Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {' CA': 4, 'NAG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {' CA': 4, 'NAG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.73, per 1000 atoms: 0.56 Number of scatterers: 13796 At special positions: 0 Unit cell: (129.47, 172.27, 108.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 132 16.00 O 2618 8.00 N 2426 7.00 C 8612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 274 " distance=2.04 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 305 " distance=2.01 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 307 " distance=2.02 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 189 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 210 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 233 " distance=2.03 Simple disulfide: pdb=" SG CYS C 244 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 258 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 316 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 304 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 426 " - pdb=" SG CYS E 430 " distance=2.03 Simple disulfide: pdb=" SG CYS E 449 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 515 " - pdb=" SG CYS E 531 " distance=2.03 Simple disulfide: pdb=" SG CYS E 519 " - pdb=" SG CYS E 541 " distance=2.03 Simple disulfide: pdb=" SG CYS E 528 " - pdb=" SG CYS E 558 " distance=2.03 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 581 " distance=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 609 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 611 " - pdb=" SG CYS E 618 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 211 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 305 " distance=2.01 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 307 " distance=2.02 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 144 " distance=2.04 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 210 " distance=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 220 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 233 " distance=2.03 Simple disulfide: pdb=" SG CYS D 244 " - pdb=" SG CYS D 275 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 316 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 304 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 142 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 243 " distance=2.03 Simple disulfide: pdb=" SG CYS F 426 " - pdb=" SG CYS F 430 " distance=2.03 Simple disulfide: pdb=" SG CYS F 449 " - pdb=" SG CYS F 478 " distance=2.03 Simple disulfide: pdb=" SG CYS F 515 " - pdb=" SG CYS F 531 " distance=2.03 Simple disulfide: pdb=" SG CYS F 519 " - pdb=" SG CYS F 541 " distance=2.03 Simple disulfide: pdb=" SG CYS F 528 " - pdb=" SG CYS F 558 " distance=2.03 Simple disulfide: pdb=" SG CYS F 565 " - pdb=" SG CYS F 581 " distance=2.03 Simple disulfide: pdb=" SG CYS F 570 " - pdb=" SG CYS F 585 " distance=2.03 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS F 620 " distance=2.03 Simple disulfide: pdb=" SG CYS F 611 " - pdb=" SG CYS F 618 " distance=2.03 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 Links applied NAG-ASN " NAG E 701 " - " ASN E 361 " " NAG E 702 " - " ASN E 336 " " NAG E 703 " - " ASN E 377 " " NAG E 704 " - " ASN E 394 " " NAG E 705 " - " ASN E 468 " " NAG E 706 " - " ASN E 367 " " NAG E 707 " - " ASN E 98 " " NAG F 701 " - " ASN F 361 " " NAG F 702 " - " ASN F 336 " " NAG F 703 " - " ASN F 377 " " NAG F 704 " - " ASN F 394 " " NAG F 705 " - " ASN F 468 " " NAG F 706 " - " ASN F 367 " " NAG F 707 " - " ASN F 98 " Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 2.0 seconds 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 34 sheets defined 23.8% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 252 through 265 removed outlier: 3.759A pdb=" N GLN A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.603A pdb=" N VAL C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 Processing helix chain 'C' and resid 163 through 177 removed outlier: 3.657A pdb=" N GLN C 176 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 188 removed outlier: 3.594A pdb=" N PHE C 188 " --> pdb=" O GLN C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.566A pdb=" N GLN C 199 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 229 Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 245 through 253 Processing helix chain 'C' and resid 255 through 260 Processing helix chain 'C' and resid 272 through 283 Processing helix chain 'C' and resid 285 through 289 removed outlier: 3.564A pdb=" N GLN C 288 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.620A pdb=" N CYS C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 102 through 113 removed outlier: 3.748A pdb=" N TRP E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 160 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 322 through 327 removed outlier: 4.038A pdb=" N GLN E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 322 through 327' Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.891A pdb=" N ALA E 432 " --> pdb=" O ASN E 429 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE E 433 " --> pdb=" O CYS E 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 433' Processing helix chain 'E' and resid 475 through 478 removed outlier: 3.510A pdb=" N CYS E 478 " --> pdb=" O ARG E 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 475 through 478' Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.582A pdb=" N ASP E 584 " --> pdb=" O CYS E 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 252 through 265 removed outlier: 3.760A pdb=" N GLN B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.603A pdb=" N VAL D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 155 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.658A pdb=" N GLN D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN D 177 " --> pdb=" O PHE D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 188 removed outlier: 3.594A pdb=" N PHE D 188 " --> pdb=" O GLN D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.566A pdb=" N GLN D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 229 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 245 through 253 Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 272 through 283 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.564A pdb=" N GLN D 288 " --> pdb=" O THR D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 removed outlier: 3.620A pdb=" N CYS D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 102 through 113 removed outlier: 3.748A pdb=" N TRP F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 160 Processing helix chain 'F' and resid 161 through 165 Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 322 through 327 removed outlier: 4.038A pdb=" N GLN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN F 327 " --> pdb=" O THR F 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 322 through 327' Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.890A pdb=" N ALA F 432 " --> pdb=" O ASN F 429 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE F 433 " --> pdb=" O CYS F 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 429 through 433' Processing helix chain 'F' and resid 475 through 478 removed outlier: 3.509A pdb=" N CYS F 478 " --> pdb=" O ARG F 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 475 through 478' Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.581A pdb=" N ASP F 584 " --> pdb=" O CYS F 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 219 removed outlier: 4.075A pdb=" N ARG A 212 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 241 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 288 removed outlier: 6.702A pdb=" N CYS A 274 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS A 307 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS A 305 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER A 278 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N MET A 282 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP A 299 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU A 284 " --> pdb=" O TYR A 297 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR A 297 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN A 286 " --> pdb=" O GLN A 295 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 295 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR A 288 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER A 293 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.749A pdb=" N TYR E 30 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU E 40 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR E 152 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.293A pdb=" N LEU E 97 " --> pdb=" O PRO E 49 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU E 94 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 71 through 72 removed outlier: 3.954A pdb=" N HIS E 81 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 174 through 177 removed outlier: 6.510A pdb=" N PHE E 174 " --> pdb=" O THR E 261 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR E 263 " --> pdb=" O PHE E 174 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 176 " --> pdb=" O TYR E 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.739A pdb=" N VAL E 223 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU E 222 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 217 " --> pdb=" O GLU E 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 278 through 283 removed outlier: 3.859A pdb=" N ALA E 279 " --> pdb=" O HIS E 392 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E 394 " --> pdb=" O ALA E 279 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER E 396 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 292 through 300 removed outlier: 7.120A pdb=" N VAL E 292 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU E 358 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA E 294 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 407 through 408 removed outlier: 6.900A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 407 through 408 removed outlier: 6.900A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 421 through 425 removed outlier: 7.155A pdb=" N GLN E 421 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL E 467 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY E 423 " --> pdb=" O LEU E 465 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU E 465 " --> pdb=" O GLY E 423 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER E 462 " --> pdb=" O SER E 457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AB7, first strand: chain 'E' and resid 589 through 591 removed outlier: 6.910A pdb=" N SER E 589 " --> pdb=" O CYS E 618 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS E 620 " --> pdb=" O SER E 589 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL E 591 " --> pdb=" O CYS E 620 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 594 through 596 Processing sheet with id=AB9, first strand: chain 'B' and resid 212 through 219 removed outlier: 4.075A pdb=" N ARG B 212 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 241 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 273 through 288 removed outlier: 6.702A pdb=" N CYS B 274 " --> pdb=" O CYS B 307 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS B 307 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N CYS B 305 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER B 278 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET B 282 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP B 299 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU B 284 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR B 297 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN B 286 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN B 295 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR B 288 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER B 293 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.749A pdb=" N TYR F 30 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU F 40 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR F 152 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.292A pdb=" N LEU F 97 " --> pdb=" O PRO F 49 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU F 94 " --> pdb=" O GLN F 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 71 through 72 removed outlier: 3.953A pdb=" N HIS F 81 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 174 through 177 removed outlier: 6.510A pdb=" N PHE F 174 " --> pdb=" O THR F 261 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR F 263 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE F 176 " --> pdb=" O TYR F 263 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.739A pdb=" N VAL F 223 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU F 222 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA F 217 " --> pdb=" O GLU F 222 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 278 through 283 removed outlier: 3.858A pdb=" N ALA F 279 " --> pdb=" O HIS F 392 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN F 394 " --> pdb=" O ALA F 279 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER F 396 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 292 through 300 removed outlier: 7.120A pdb=" N VAL F 292 " --> pdb=" O LEU F 358 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU F 358 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA F 294 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 407 through 408 removed outlier: 6.899A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 407 through 408 removed outlier: 6.899A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 421 through 425 removed outlier: 7.154A pdb=" N GLN F 421 " --> pdb=" O VAL F 467 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL F 467 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY F 423 " --> pdb=" O LEU F 465 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU F 465 " --> pdb=" O GLY F 423 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER F 462 " --> pdb=" O SER F 457 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD6, first strand: chain 'F' and resid 589 through 591 removed outlier: 6.910A pdb=" N SER F 589 " --> pdb=" O CYS F 618 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS F 620 " --> pdb=" O SER F 589 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL F 591 " --> pdb=" O CYS F 620 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 594 through 596 424 hydrogen bonds defined for protein. 1176 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: 4.01 Time building geometry restraints manager: 5.46 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: 4577 1.34 - 1.47: 3332 1.47 - 1.59: 6031 1.59 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 14090 Sorted by residual: bond pdb=" N HIS C 253 " pdb=" CA HIS C 253 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.46e+00 bond pdb=" N HIS D 253 " pdb=" CA HIS D 253 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.27e+00 bond pdb=" C CYS E 565 " pdb=" N PRO E 566 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.21e+00 bond pdb=" C CYS F 565 " pdb=" N PRO F 566 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.12e+00 bond pdb=" CB ASP E 378 " pdb=" CG ASP E 378 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.10e+00 ... (remaining 14085 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.53: 518 106.53 - 113.71: 7892 113.71 - 120.89: 6161 120.89 - 128.07: 4443 128.07 - 135.25: 126 Bond angle restraints: 19140 Sorted by residual: angle pdb=" C VAL F 303 " pdb=" N VAL F 304 " pdb=" CA VAL F 304 " ideal model delta sigma weight residual 120.24 125.00 -4.76 6.30e-01 2.52e+00 5.71e+01 angle pdb=" C VAL E 303 " pdb=" N VAL E 304 " pdb=" CA VAL E 304 " ideal model delta sigma weight residual 120.24 125.00 -4.76 6.30e-01 2.52e+00 5.71e+01 angle pdb=" C CYS C 252 " pdb=" N HIS C 253 " pdb=" CA HIS C 253 " ideal model delta sigma weight residual 121.54 132.37 -10.83 1.91e+00 2.74e-01 3.21e+01 angle pdb=" C CYS D 252 " pdb=" N HIS D 253 " pdb=" CA HIS D 253 " ideal model delta sigma weight residual 121.54 132.36 -10.82 1.91e+00 2.74e-01 3.21e+01 angle pdb=" N ASP E 584 " pdb=" CA ASP E 584 " pdb=" C ASP E 584 " ideal model delta sigma weight residual 114.09 106.53 7.56 1.55e+00 4.16e-01 2.38e+01 ... (remaining 19135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 8294 16.65 - 33.29: 293 33.29 - 49.94: 52 49.94 - 66.59: 4 66.59 - 83.23: 8 Dihedral angle restraints: 8651 sinusoidal: 3579 harmonic: 5072 Sorted by residual: dihedral pdb=" CB CYS F 426 " pdb=" SG CYS F 426 " pdb=" SG CYS F 430 " pdb=" CB CYS F 430 " ideal model delta sinusoidal sigma weight residual -86.00 -169.23 83.23 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS E 426 " pdb=" SG CYS E 426 " pdb=" SG CYS E 430 " pdb=" CB CYS E 430 " ideal model delta sinusoidal sigma weight residual -86.00 -169.21 83.21 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS C 191 " pdb=" SG CYS C 191 " pdb=" SG CYS C 198 " pdb=" CB CYS C 198 " ideal model delta sinusoidal sigma weight residual -86.00 -168.97 82.97 1 1.00e+01 1.00e-02 8.43e+01 ... (remaining 8648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1988 0.097 - 0.194: 190 0.194 - 0.292: 2 0.292 - 0.389: 0 0.389 - 0.486: 6 Chirality restraints: 2186 Sorted by residual: chirality pdb=" C1 NAG E 706 " pdb=" ND2 ASN E 367 " pdb=" C2 NAG E 706 " pdb=" O5 NAG E 706 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" C1 NAG F 706 " pdb=" ND2 ASN F 367 " pdb=" C2 NAG F 706 " pdb=" O5 NAG F 706 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" C1 NAG E 705 " pdb=" ND2 ASN E 468 " pdb=" C2 NAG E 705 " pdb=" O5 NAG E 705 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 2183 not shown) Planarity restraints: 2492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 275 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO B 276 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 275 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 276 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 598 " 0.039 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO F 599 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 599 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 599 " 0.034 5.00e-02 4.00e+02 ... (remaining 2489 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 24 2.32 - 2.97: 6014 2.97 - 3.61: 18089 3.61 - 4.26: 29216 4.26 - 4.90: 48607 Nonbonded interactions: 101950 Sorted by model distance: nonbonded pdb=" OD1 ASP E 230 " pdb=" OE1 GLU E 232 " model vdw 1.677 3.040 nonbonded pdb=" OD1 ASP F 230 " pdb=" OE1 GLU F 232 " model vdw 1.677 3.040 nonbonded pdb=" OD1 ASP F 567 " pdb=" OD2 ASP F 584 " model vdw 1.917 3.040 nonbonded pdb=" OD1 ASP E 567 " pdb=" OD2 ASP E 584 " model vdw 1.918 3.040 nonbonded pdb=" O HIS F 569 " pdb=" OD2 ASP F 584 " model vdw 2.111 3.040 ... (remaining 101945 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 132 5.16 5 C 8612 2.51 5 N 2426 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.010 Extract box with map and model: 4.220 Check model and map are aligned: 0.200 Process input model: 35.080 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2803 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 : 0.006 0.061 14090 Z= 0.362 Angle : 0.964 10.937 19140 Z= 0.551 Chirality : 0.059 0.486 2186 Planarity : 0.007 0.061 2478 Dihedral : 8.647 70.338 5186 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.04 % Favored : 94.84 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -3.22 (0.18), residues: 1706 helix: -2.97 (0.19), residues: 346 sheet: -1.09 (0.24), residues: 436 loop : -2.35 (0.18), residues: 924 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 325 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.3201 time to fit residues: 142.2260 Evaluate side-chains 138 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 286 GLN C 184 GLN C 200 GLN C 228 GLN C 241 GLN E 84 ASN E 333 HIS ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 490 GLN ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 579 ASN B 236 GLN ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 594 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4048 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 14090 Z= 0.362 Angle : 0.883 11.086 19140 Z= 0.463 Chirality : 0.052 0.372 2186 Planarity : 0.007 0.068 2478 Dihedral : 6.141 26.683 1972 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -2.71 (0.19), residues: 1706 helix: -2.12 (0.23), residues: 372 sheet: -1.10 (0.23), residues: 470 loop : -2.02 (0.20), residues: 864 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 212 average time/residue: 0.2625 time to fit residues: 81.3156 Evaluate side-chains 144 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1155 time to fit residues: 2.4352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 0.0050 chunk 48 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 169 optimal weight: 0.1980 chunk 139 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 125 optimal weight: 0.0050 overall best weight: 0.8412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN E 443 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 184 GLN D 236 HIS ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4073 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 14090 Z= 0.184 Angle : 0.642 12.545 19140 Z= 0.327 Chirality : 0.048 0.342 2186 Planarity : 0.005 0.051 2478 Dihedral : 5.428 25.187 1972 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.57 % Favored : 94.37 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -2.09 (0.19), residues: 1706 helix: -1.06 (0.26), residues: 348 sheet: -1.01 (0.23), residues: 502 loop : -1.71 (0.20), residues: 856 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.2484 time to fit residues: 70.5372 Evaluate side-chains 130 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 166 optimal weight: 0.2980 chunk 82 optimal weight: 0.0030 chunk 148 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN E 44 GLN E 429 ASN ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 236 HIS ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4429 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 14090 Z= 0.214 Angle : 0.657 12.840 19140 Z= 0.337 Chirality : 0.047 0.333 2186 Planarity : 0.005 0.055 2478 Dihedral : 5.304 21.740 1972 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -2.04 (0.19), residues: 1706 helix: -1.09 (0.26), residues: 378 sheet: -0.93 (0.23), residues: 488 loop : -1.68 (0.20), residues: 840 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2506 time to fit residues: 71.9690 Evaluate side-chains 130 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 265 GLN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4644 moved from start: 0.7024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14090 Z= 0.202 Angle : 0.674 13.942 19140 Z= 0.340 Chirality : 0.047 0.314 2186 Planarity : 0.005 0.065 2478 Dihedral : 5.173 22.600 1972 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.86 (0.20), residues: 1706 helix: -0.94 (0.26), residues: 368 sheet: -0.86 (0.24), residues: 470 loop : -1.53 (0.20), residues: 868 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.716 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 outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2621 time to fit residues: 77.0329 Evaluate side-chains 124 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 166 optimal weight: 0.2980 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 0.0010 chunk 13 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN E 44 GLN E 246 HIS E 495 GLN E 583 GLN D 147 GLN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4622 moved from start: 0.7329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 14090 Z= 0.171 Angle : 0.640 19.940 19140 Z= 0.320 Chirality : 0.046 0.307 2186 Planarity : 0.005 0.054 2478 Dihedral : 4.894 26.241 1972 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.62 (0.20), residues: 1706 helix: -0.68 (0.27), residues: 366 sheet: -0.71 (0.25), residues: 450 loop : -1.41 (0.20), residues: 890 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2537 time to fit residues: 70.1634 Evaluate side-chains 127 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 101 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 583 GLN D 147 GLN D 177 ASN D 228 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4973 moved from start: 0.8396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 14090 Z= 0.252 Angle : 0.714 17.639 19140 Z= 0.359 Chirality : 0.048 0.313 2186 Planarity : 0.005 0.051 2478 Dihedral : 5.174 26.890 1972 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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 (0.20), residues: 1706 helix: -0.94 (0.26), residues: 370 sheet: -0.82 (0.24), residues: 466 loop : -1.45 (0.20), residues: 870 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2663 time to fit residues: 73.3932 Evaluate side-chains 132 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 0.0870 chunk 105 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 583 GLN ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 moved from start: 0.8701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 14090 Z= 0.169 Angle : 0.655 17.954 19140 Z= 0.323 Chirality : 0.046 0.296 2186 Planarity : 0.004 0.051 2478 Dihedral : 4.886 24.761 1972 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.65 (0.20), residues: 1706 helix: -0.83 (0.26), residues: 370 sheet: -0.74 (0.24), residues: 474 loop : -1.37 (0.21), residues: 862 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2633 time to fit residues: 72.4964 Evaluate side-chains 134 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 153 optimal weight: 0.0770 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 0.0570 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 583 GLN ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4924 moved from start: 0.8891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 14090 Z= 0.160 Angle : 0.664 17.271 19140 Z= 0.327 Chirality : 0.046 0.288 2186 Planarity : 0.004 0.051 2478 Dihedral : 4.804 24.031 1972 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.52 (0.20), residues: 1706 helix: -0.64 (0.27), residues: 370 sheet: -0.64 (0.25), residues: 448 loop : -1.32 (0.20), residues: 888 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2680 time to fit residues: 70.9441 Evaluate side-chains 137 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.614 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 136 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 583 GLN B 236 GLN ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5046 moved from start: 0.9364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 14090 Z= 0.191 Angle : 0.666 16.886 19140 Z= 0.332 Chirality : 0.046 0.290 2186 Planarity : 0.004 0.046 2478 Dihedral : 4.841 24.138 1972 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.48 (0.20), residues: 1706 helix: -0.64 (0.27), residues: 370 sheet: -0.65 (0.25), residues: 448 loop : -1.24 (0.21), residues: 888 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2704 time to fit residues: 73.4449 Evaluate side-chains 132 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.476 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 136 optimal weight: 0.0980 chunk 57 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 ASN E 44 GLN E 70 GLN E 482 HIS E 583 GLN B 256 GLN D 147 GLN D 166 GLN ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.171083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.149107 restraints weight = 40706.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.148530 restraints weight = 43755.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.149801 restraints weight = 38990.017| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 1.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 14090 Z= 0.318 Angle : 0.823 17.175 19140 Z= 0.422 Chirality : 0.051 0.327 2186 Planarity : 0.007 0.225 2478 Dihedral : 5.692 34.862 1972 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.27 % Favored : 92.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.90 (0.20), residues: 1706 helix: -1.26 (0.26), residues: 368 sheet: -0.84 (0.25), residues: 432 loop : -1.43 (0.20), residues: 906 =============================================================================== Job complete usr+sys time: 2446.51 seconds wall clock time: 48 minutes 58.28 seconds (2938.28 seconds total)