Starting phenix.real_space_refine on Sat Mar 16 05:46:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2j_20572/03_2024/6q2j_20572_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2j_20572/03_2024/6q2j_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_20572/03_2024/6q2j_20572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2j_20572/03_2024/6q2j_20572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2j_20572/03_2024/6q2j_20572_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2j_20572/03_2024/6q2j_20572_neut.pdb" } resolution = 4.1 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= 0.006 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 21 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 7.01, per 1000 atoms: 0.51 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: 5.51 Conformation dependent library (CDL) restraints added in 2.6 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: 1.85 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: 4.38 Time building geometry restraints manager: 6.01 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=" C1 NAG E 707 " pdb=" O5 NAG E 707 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" C1 NAG F 707 " pdb=" O5 NAG F 707 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 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=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.09e+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: 8472 16.65 - 33.29: 305 33.29 - 49.94: 68 49.94 - 66.59: 8 66.59 - 83.23: 8 Dihedral angle restraints: 8861 sinusoidal: 3789 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 8858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1984 0.097 - 0.194: 194 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 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: 1.080 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: 5.540 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 37.950 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2844 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= 0.378 Angle : 0.978 10.937 19140 Z= 0.553 Chirality : 0.059 0.486 2186 Planarity : 0.007 0.061 2478 Dihedral : 9.003 70.338 5396 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 % Allowed : 1.70 % Favored : 98.17 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP E 334 HIS 0.006 0.001 HIS D 253 PHE 0.025 0.003 PHE F 258 TYR 0.032 0.003 TYR E 263 ARG 0.008 0.001 ARG F 355 *********************** 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 : 1.665 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: C 299 SER cc_start: 0.7256 (p) cc_final: 0.5982 (t) REVERT: D 310 MET cc_start: -0.0991 (mtm) cc_final: -0.2766 (mmp) REVERT: F 255 MET cc_start: -0.2474 (ptp) cc_final: -0.4322 (mtm) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.3209 time to fit residues: 141.5221 Evaluate side-chains 139 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 265 GLN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4128 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 14090 Z= 0.327 Angle : 0.841 10.294 19140 Z= 0.434 Chirality : 0.053 0.432 2186 Planarity : 0.007 0.078 2478 Dihedral : 7.150 59.209 2182 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.26 % Allowed : 3.79 % Favored : 95.95 % 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: -2.67 (0.19), residues: 1706 helix: -2.05 (0.23), residues: 372 sheet: -1.09 (0.23), residues: 470 loop : -2.00 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 334 HIS 0.023 0.003 HIS D 253 PHE 0.026 0.003 PHE D 188 TYR 0.032 0.003 TYR B 297 ARG 0.009 0.001 ARG C 313 *********************** 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 211 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LEU cc_start: 0.2700 (mt) cc_final: 0.2030 (pt) REVERT: C 185 MET cc_start: 0.6635 (mtp) cc_final: 0.5987 (mmm) REVERT: C 196 ILE cc_start: 0.7758 (tp) cc_final: 0.7521 (pt) REVERT: C 299 SER cc_start: 0.7882 (p) cc_final: 0.7424 (m) REVERT: C 310 MET cc_start: 0.8154 (mtm) cc_final: 0.7767 (mtm) REVERT: E 486 VAL cc_start: 0.6649 (t) cc_final: 0.5938 (t) REVERT: B 228 TRP cc_start: 0.4522 (p-90) cc_final: 0.2832 (p-90) REVERT: B 253 MET cc_start: 0.6556 (ptm) cc_final: 0.6100 (ptt) REVERT: D 310 MET cc_start: 0.0478 (mtm) cc_final: -0.0961 (mmp) REVERT: F 255 MET cc_start: -0.2596 (ptp) cc_final: -0.4903 (mtt) REVERT: F 333 HIS cc_start: -0.0255 (OUTLIER) cc_final: -0.1281 (p-80) outliers start: 4 outliers final: 0 residues processed: 211 average time/residue: 0.2706 time to fit residues: 83.4251 Evaluate side-chains 141 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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: 0.0370 chunk 48 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 125 optimal weight: 0.0050 overall best weight: 2.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 429 ASN E 443 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 184 GLN D 228 GLN D 265 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4771 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 14090 Z= 0.329 Angle : 0.803 10.589 19140 Z= 0.418 Chirality : 0.053 0.372 2186 Planarity : 0.007 0.141 2478 Dihedral : 6.611 46.870 2182 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.98 % Favored : 92.91 % Rotamer: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.89 % 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: -2.39 (0.19), residues: 1706 helix: -1.58 (0.25), residues: 362 sheet: -1.19 (0.23), residues: 496 loop : -1.77 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 139 HIS 0.014 0.002 HIS A 306 PHE 0.024 0.002 PHE F 116 TYR 0.029 0.003 TYR D 279 ARG 0.038 0.001 ARG E 587 *********************** 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 227 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 1.562 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: C 185 MET cc_start: 0.6539 (mtp) cc_final: 0.6097 (mmm) REVERT: C 196 ILE cc_start: 0.7918 (tp) cc_final: 0.7687 (tp) REVERT: C 299 SER cc_start: 0.7350 (p) cc_final: 0.6713 (m) REVERT: C 305 LYS cc_start: 0.7213 (mtpt) cc_final: 0.6846 (mtmt) REVERT: E 39 LYS cc_start: 0.6652 (mttt) cc_final: 0.6119 (mmtt) REVERT: B 228 TRP cc_start: 0.6516 (p-90) cc_final: 0.5607 (p-90) REVERT: D 168 GLN cc_start: 0.4088 (mm110) cc_final: 0.3408 (mm-40) REVERT: D 245 TRP cc_start: 0.2311 (m100) cc_final: 0.2046 (m100) REVERT: D 310 MET cc_start: 0.2211 (mtm) cc_final: 0.0201 (mmt) REVERT: F 255 MET cc_start: -0.2976 (ptp) cc_final: -0.3960 (mtt) REVERT: F 579 ASN cc_start: 0.6873 (p0) cc_final: 0.6442 (m-40) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.2719 time to fit residues: 88.8580 Evaluate side-chains 142 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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: 7.9990 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 257 ASN E 70 GLN ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN D 147 GLN D 236 HIS ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5248 moved from start: 0.8778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14090 Z= 0.346 Angle : 0.844 14.883 19140 Z= 0.437 Chirality : 0.053 0.390 2186 Planarity : 0.007 0.106 2478 Dihedral : 6.676 49.698 2182 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.26 % Allowed : 4.70 % Favored : 95.04 % 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: -2.55 (0.19), residues: 1706 helix: -1.87 (0.24), residues: 378 sheet: -1.22 (0.24), residues: 428 loop : -1.82 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 334 HIS 0.009 0.002 HIS E 569 PHE 0.028 0.003 PHE F 555 TYR 0.031 0.003 TYR E 146 ARG 0.009 0.001 ARG C 250 *********************** 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 200 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 196 time to evaluate : 1.594 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: C 214 MET cc_start: 0.7782 (mmp) cc_final: 0.7085 (mtp) REVERT: C 301 GLU cc_start: 0.6351 (tm-30) cc_final: 0.6102 (tp30) REVERT: C 305 LYS cc_start: 0.7515 (mtpt) cc_final: 0.7165 (mtmt) REVERT: C 307 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: B 258 LYS cc_start: 0.8018 (mttt) cc_final: 0.7762 (mttt) REVERT: B 299 ASP cc_start: 0.7875 (p0) cc_final: 0.7635 (p0) REVERT: D 145 ASN cc_start: 0.6201 (t0) cc_final: 0.5958 (t0) REVERT: D 178 ILE cc_start: 0.6785 (pt) cc_final: 0.6457 (pt) REVERT: D 188 PHE cc_start: 0.6376 (t80) cc_final: 0.6129 (m-80) REVERT: F 255 MET cc_start: -0.2915 (ptp) cc_final: -0.4445 (mtt) REVERT: F 422 ILE cc_start: 0.5736 (mt) cc_final: 0.5321 (mm) REVERT: F 523 LYS cc_start: 0.7842 (ptmt) cc_final: 0.7388 (pttp) outliers start: 4 outliers final: 1 residues processed: 199 average time/residue: 0.2686 time to fit residues: 76.6409 Evaluate side-chains 141 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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: 8.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5149 moved from start: 0.9066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14090 Z= 0.198 Angle : 0.695 15.499 19140 Z= 0.348 Chirality : 0.048 0.414 2186 Planarity : 0.005 0.077 2478 Dihedral : 5.938 49.722 2182 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.07 % Allowed : 2.22 % Favored : 97.72 % 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: -2.26 (0.19), residues: 1706 helix: -1.43 (0.25), residues: 394 sheet: -1.11 (0.23), residues: 478 loop : -1.70 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 334 HIS 0.005 0.001 HIS A 214 PHE 0.024 0.002 PHE C 307 TYR 0.014 0.001 TYR E 122 ARG 0.007 0.000 ARG F 171 *********************** 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 189 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 1.694 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: C 214 MET cc_start: 0.7700 (mmp) cc_final: 0.6884 (mtp) REVERT: C 305 LYS cc_start: 0.7475 (mtpt) cc_final: 0.7026 (mtmt) REVERT: B 231 SER cc_start: 0.7748 (t) cc_final: 0.7518 (p) REVERT: B 258 LYS cc_start: 0.8022 (mttt) cc_final: 0.7710 (mttt) REVERT: B 299 ASP cc_start: 0.7726 (p0) cc_final: 0.7073 (p0) REVERT: D 245 TRP cc_start: 0.2618 (m100) cc_final: 0.2253 (m100) REVERT: F 237 TYR cc_start: 0.1901 (m-80) cc_final: 0.1488 (m-80) REVERT: F 255 MET cc_start: -0.2865 (ptp) cc_final: -0.3447 (mtt) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.2823 time to fit residues: 76.9886 Evaluate side-chains 138 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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: 10.0000 chunk 149 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 166 optimal weight: 0.0030 chunk 138 optimal weight: 0.0060 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 overall best weight: 1.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5235 moved from start: 0.9506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 14090 Z= 0.225 Angle : 0.710 20.363 19140 Z= 0.357 Chirality : 0.048 0.352 2186 Planarity : 0.005 0.073 2478 Dihedral : 5.713 47.765 2182 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.07 % Allowed : 2.02 % Favored : 97.91 % 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: -2.12 (0.19), residues: 1706 helix: -1.34 (0.25), residues: 394 sheet: -0.95 (0.23), residues: 472 loop : -1.64 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 334 HIS 0.009 0.001 HIS F 569 PHE 0.025 0.002 PHE D 173 TYR 0.015 0.002 TYR E 146 ARG 0.005 0.000 ARG F 525 *********************** 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 191 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.640 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: C 185 MET cc_start: 0.6847 (mtp) cc_final: 0.6446 (mmm) REVERT: C 214 MET cc_start: 0.7700 (mmp) cc_final: 0.7005 (mtp) REVERT: C 305 LYS cc_start: 0.7517 (mtpt) cc_final: 0.7034 (mtmt) REVERT: B 231 SER cc_start: 0.8003 (t) cc_final: 0.7688 (p) REVERT: D 178 ILE cc_start: 0.6909 (pt) cc_final: 0.6636 (pt) REVERT: D 245 TRP cc_start: 0.2664 (m100) cc_final: 0.2202 (m100) REVERT: F 237 TYR cc_start: 0.2036 (m-80) cc_final: 0.1707 (m-80) REVERT: F 255 MET cc_start: -0.2869 (ptp) cc_final: -0.3794 (mtm) outliers start: 1 outliers final: 1 residues processed: 191 average time/residue: 0.2667 time to fit residues: 73.9749 Evaluate side-chains 141 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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: 3.9990 chunk 94 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN E 246 HIS ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN D 228 GLN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5281 moved from start: 0.9880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 14090 Z= 0.217 Angle : 0.687 19.446 19140 Z= 0.344 Chirality : 0.047 0.321 2186 Planarity : 0.005 0.061 2478 Dihedral : 5.541 47.114 2182 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: -1.89 (0.20), residues: 1706 helix: -0.97 (0.27), residues: 370 sheet: -0.92 (0.24), residues: 456 loop : -1.51 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 228 HIS 0.013 0.001 HIS F 569 PHE 0.028 0.002 PHE C 307 TYR 0.036 0.002 TYR E 263 ARG 0.008 0.000 ARG E 313 *********************** 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 189 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.492 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: A 267 ASP cc_start: 0.6775 (m-30) cc_final: 0.6544 (t70) REVERT: C 185 MET cc_start: 0.6835 (mtp) cc_final: 0.6431 (mmm) REVERT: C 214 MET cc_start: 0.7706 (mmp) cc_final: 0.7043 (mtp) REVERT: C 305 LYS cc_start: 0.7567 (mtpt) cc_final: 0.7117 (mtmt) REVERT: E 497 GLN cc_start: 0.6873 (mm-40) cc_final: 0.6495 (mm-40) REVERT: B 231 SER cc_start: 0.8078 (t) cc_final: 0.7825 (p) REVERT: B 299 ASP cc_start: 0.7782 (p0) cc_final: 0.7311 (p0) REVERT: D 178 ILE cc_start: 0.6966 (pt) cc_final: 0.6735 (pt) REVERT: D 245 TRP cc_start: 0.2680 (m100) cc_final: 0.2156 (m100) REVERT: D 310 MET cc_start: 0.2386 (mtp) cc_final: 0.1928 (mtm) REVERT: F 237 TYR cc_start: 0.1981 (m-80) cc_final: 0.1706 (m-80) REVERT: F 255 MET cc_start: -0.2897 (ptp) cc_final: -0.3461 (mtt) REVERT: F 523 LYS cc_start: 0.7930 (ptmt) cc_final: 0.7585 (pttp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2542 time to fit residues: 70.7062 Evaluate side-chains 144 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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: 7.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 0.1980 chunk 15 optimal weight: 20.0000 chunk 130 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN E 352 HIS ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN B 236 GLN D 228 GLN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 moved from start: 1.0450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14090 Z= 0.210 Angle : 0.686 18.547 19140 Z= 0.343 Chirality : 0.047 0.304 2186 Planarity : 0.005 0.060 2478 Dihedral : 5.377 45.481 2182 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: -1.85 (0.20), residues: 1706 helix: -1.07 (0.26), residues: 382 sheet: -0.75 (0.26), residues: 402 loop : -1.49 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 85 HIS 0.005 0.001 HIS D 236 PHE 0.036 0.002 PHE D 173 TYR 0.013 0.002 TYR E 146 ARG 0.004 0.000 ARG B 233 *********************** 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 183 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.7774 (t80) cc_final: 0.7341 (t80) REVERT: A 267 ASP cc_start: 0.6592 (m-30) cc_final: 0.6298 (t70) REVERT: C 133 GLU cc_start: 0.8243 (tp30) cc_final: 0.7850 (tp30) REVERT: C 134 VAL cc_start: 0.7078 (t) cc_final: 0.6858 (t) REVERT: C 185 MET cc_start: 0.6833 (mtp) cc_final: 0.6492 (mmm) REVERT: C 214 MET cc_start: 0.7598 (mmp) cc_final: 0.7027 (mtp) REVERT: C 305 LYS cc_start: 0.7629 (mtpt) cc_final: 0.6936 (mtpt) REVERT: B 299 ASP cc_start: 0.7850 (p0) cc_final: 0.7455 (p0) REVERT: D 178 ILE cc_start: 0.7346 (pt) cc_final: 0.7141 (pt) REVERT: D 245 TRP cc_start: 0.2854 (m100) cc_final: 0.2396 (m100) REVERT: D 310 MET cc_start: 0.2802 (mtp) cc_final: 0.2112 (mmp) REVERT: F 237 TYR cc_start: 0.2101 (m-80) cc_final: 0.1901 (m-80) REVERT: F 255 MET cc_start: -0.3005 (ptp) cc_final: -0.3281 (mtm) REVERT: F 370 MET cc_start: -0.0782 (mmm) cc_final: -0.1945 (tpt) REVERT: F 523 LYS cc_start: 0.7755 (ptmt) cc_final: 0.7509 (pttp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2591 time to fit residues: 69.4218 Evaluate side-chains 143 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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: 4.9990 chunk 158 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 482 HIS E 495 GLN E 579 ASN ** E 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5685 moved from start: 1.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 14090 Z= 0.365 Angle : 0.875 18.574 19140 Z= 0.444 Chirality : 0.052 0.329 2186 Planarity : 0.006 0.064 2478 Dihedral : 6.360 49.296 2182 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -2.25 (0.19), residues: 1706 helix: -1.48 (0.26), residues: 366 sheet: -0.97 (0.25), residues: 426 loop : -1.73 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 334 HIS 0.014 0.002 HIS A 214 PHE 0.021 0.003 PHE F 258 TYR 0.021 0.003 TYR A 297 ARG 0.008 0.001 ARG B 233 *********************** 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 186 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 PHE cc_start: 0.8316 (t80) cc_final: 0.7663 (t80) REVERT: A 253 MET cc_start: 0.8881 (mtp) cc_final: 0.8665 (mtp) REVERT: A 304 ASP cc_start: 0.8272 (p0) cc_final: 0.7984 (p0) REVERT: C 133 GLU cc_start: 0.8284 (tp30) cc_final: 0.7886 (tp30) REVERT: C 214 MET cc_start: 0.7720 (mmp) cc_final: 0.7126 (mtp) REVERT: C 305 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7348 (mtmt) REVERT: B 299 ASP cc_start: 0.7722 (p0) cc_final: 0.7460 (p0) REVERT: D 166 GLN cc_start: 0.7869 (tm130) cc_final: 0.7539 (pp30) REVERT: F 255 MET cc_start: -0.2915 (ptp) cc_final: -0.3213 (mtm) REVERT: F 583 GLN cc_start: 0.5877 (pp30) cc_final: 0.5323 (pt0) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2521 time to fit residues: 69.8268 Evaluate side-chains 134 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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: 4.9990 chunk 77 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 583 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5572 moved from start: 1.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14090 Z= 0.199 Angle : 0.711 20.143 19140 Z= 0.358 Chirality : 0.048 0.325 2186 Planarity : 0.005 0.062 2478 Dihedral : 5.704 48.470 2182 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -1.93 (0.20), residues: 1706 helix: -1.07 (0.26), residues: 362 sheet: -0.79 (0.26), residues: 400 loop : -1.59 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 85 HIS 0.005 0.001 HIS F 569 PHE 0.034 0.002 PHE C 307 TYR 0.021 0.002 TYR D 151 ARG 0.007 0.000 ARG F 553 ********************** 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 181 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.629 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: A 248 PHE cc_start: 0.8207 (t80) cc_final: 0.7646 (t80) REVERT: C 133 GLU cc_start: 0.8096 (tp30) cc_final: 0.7813 (tp30) REVERT: C 214 MET cc_start: 0.7579 (mmp) cc_final: 0.7161 (mtp) REVERT: C 305 LYS cc_start: 0.7740 (mtpt) cc_final: 0.7412 (mtmt) REVERT: B 229 VAL cc_start: 0.5587 (p) cc_final: 0.5341 (p) REVERT: B 253 MET cc_start: 0.8543 (ptp) cc_final: 0.8274 (ptm) REVERT: B 299 ASP cc_start: 0.7863 (p0) cc_final: 0.7590 (p0) REVERT: F 237 TYR cc_start: 0.2913 (m-80) cc_final: 0.2330 (m-80) REVERT: F 255 MET cc_start: -0.2854 (ptp) cc_final: -0.3189 (mtm) REVERT: F 583 GLN cc_start: 0.5582 (pp30) cc_final: 0.4710 (pt0) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2531 time to fit residues: 67.7290 Evaluate side-chains 135 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.616 ------------------------------------------------------------------------------- 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: 9.9990 chunk 125 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 0.0770 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 7 optimal weight: 0.0040 overall best weight: 1.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 583 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.168893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.146992 restraints weight = 41234.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.148247 restraints weight = 37025.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.149030 restraints weight = 32727.396| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 1.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14090 Z= 0.191 Angle : 0.688 19.474 19140 Z= 0.345 Chirality : 0.047 0.317 2186 Planarity : 0.005 0.062 2478 Dihedral : 5.421 45.446 2182 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -1.78 (0.20), residues: 1706 helix: -0.99 (0.26), residues: 362 sheet: -0.67 (0.26), residues: 400 loop : -1.48 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 85 HIS 0.005 0.001 HIS F 569 PHE 0.031 0.002 PHE C 307 TYR 0.033 0.002 TYR F 36 ARG 0.005 0.000 ARG F 553 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.84 seconds wall clock time: 48 minutes 30.07 seconds (2910.07 seconds total)