Starting phenix.real_space_refine on Sat Mar 16 17:22:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/03_2024/6q2o_20576_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/03_2024/6q2o_20576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/03_2024/6q2o_20576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/03_2024/6q2o_20576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/03_2024/6q2o_20576_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/03_2024/6q2o_20576_neut.pdb" } resolution = 3.65 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= 0.003 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 138 5.16 5 C 9434 2.51 5 N 2738 2.21 5 O 2878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 97": "NH1" <-> "NH2" Residue "C TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 205": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 415": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 97": "NH1" <-> "NH2" Residue "D TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 415": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15196 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "C" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 3 Chain: "E" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4499 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 537} Chain breaks: 4 Chain: "D" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 3 Chain: "F" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4499 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 537} Chain breaks: 4 Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.87, per 1000 atoms: 0.52 Number of scatterers: 15196 At special positions: 0 Unit cell: (128.4, 200.09, 102.72, 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 138 16.00 O 2878 8.00 N 2738 7.00 C 9434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 194 " distance=2.02 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 194 " distance=2.02 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 222 " distance=2.02 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 174 " distance=2.02 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 200 " distance=2.02 Simple disulfide: pdb=" SG CYS C 195 " - pdb=" SG CYS C 241 " distance=2.02 Simple disulfide: pdb=" SG CYS C 224 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 258 " - pdb=" SG CYS C 264 " distance=2.04 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 347 " 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=2.02 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 D 40 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 222 " distance=2.02 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 200 " distance=2.02 Simple disulfide: pdb=" SG CYS D 195 " - pdb=" SG CYS D 241 " distance=2.02 Simple disulfide: pdb=" SG CYS D 224 " - pdb=" SG CYS D 229 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 258 " - pdb=" SG CYS D 264 " distance=2.04 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 347 " 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=2.02 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 E2005 " - " ASN E 377 " " NAG E2006 " - " ASN E 394 " " NAG E2007 " - " ASN E 468 " " NAG E2008 " - " ASN E 367 " " NAG E2009 " - " ASN E 336 " " NAG E2010 " - " ASN E 361 " " NAG F2005 " - " ASN F 377 " " NAG F2006 " - " ASN F 394 " " NAG F2007 " - " ASN F 468 " " NAG F2008 " - " ASN F 367 " " NAG F2009 " - " ASN F 336 " " NAG F2010 " - " ASN F 361 " Time building additional restraints: 5.50 Conformation dependent library (CDL) restraints added in 2.9 seconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 36 sheets defined 26.8% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 113 through 116 removed outlier: 3.695A pdb=" N GLY A 116 " --> pdb=" O SER A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'B' and resid 113 through 116 removed outlier: 3.695A pdb=" N GLY B 116 " --> pdb=" O SER B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'C' and resid 39 through 48 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 101 through 110 removed outlier: 3.547A pdb=" N CYS C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 173 through 186 Processing helix chain 'C' and resid 196 through 208 Processing helix chain 'C' and resid 212 through 221 removed outlier: 3.623A pdb=" N THR C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET C 219 " --> pdb=" O TYR C 215 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.738A pdb=" N ALA C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.659A pdb=" N ASP C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 275 removed outlier: 3.655A pdb=" N ASN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS C 275 " --> pdb=" O PHE C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 288 Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.592A pdb=" N CYS C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 344 removed outlier: 3.863A pdb=" N ASP C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.508A pdb=" N TRP E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 167 removed outlier: 3.924A pdb=" N PHE E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'E' and resid 322 through 328 removed outlier: 3.595A pdb=" N GLN E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.764A pdb=" N ALA E 432 " --> pdb=" O ASN E 429 " (cutoff:3.500A) removed outlier: 3.869A 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 470 through 475 removed outlier: 3.640A pdb=" N ARG E 475 " --> pdb=" O LYS E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 530 Processing helix chain 'E' and resid 564 through 568 removed outlier: 3.963A pdb=" N ASP E 567 " --> pdb=" O THR E 564 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY E 568 " --> pdb=" O CYS E 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 564 through 568' Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.580A pdb=" N ASP E 584 " --> pdb=" O CYS E 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 48 Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 101 through 110 removed outlier: 3.546A pdb=" N CYS D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 173 through 186 Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.623A pdb=" N THR D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 217 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET D 219 " --> pdb=" O TYR D 215 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 220 " --> pdb=" O THR D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 235 removed outlier: 3.738A pdb=" N ALA D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.659A pdb=" N ASP D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 275 removed outlier: 3.655A pdb=" N ASN D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS D 275 " --> pdb=" O PHE D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 288 Processing helix chain 'D' and resid 289 through 299 removed outlier: 3.592A pdb=" N CYS D 293 " --> pdb=" O ASN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 344 removed outlier: 3.864A pdb=" N ASP D 341 " --> pdb=" O LYS D 337 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 357 Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.507A pdb=" N TRP F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 3.925A pdb=" N PHE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'F' and resid 322 through 328 removed outlier: 3.596A pdb=" N GLN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.764A pdb=" N ALA F 432 " --> pdb=" O ASN F 429 " (cutoff:3.500A) removed outlier: 3.869A 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 470 through 475 removed outlier: 3.640A pdb=" N ARG F 475 " --> pdb=" O LYS F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 530 Processing helix chain 'F' and resid 564 through 568 removed outlier: 3.963A pdb=" N ASP F 567 " --> pdb=" O THR F 564 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY F 568 " --> pdb=" O CYS F 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 564 through 568' Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.580A pdb=" N ASP F 584 " --> pdb=" O CYS F 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 111 Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.646A pdb=" N ARG A 166 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 195 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLU A 193 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR A 170 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA A 191 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 176 Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 111 Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 170 removed outlier: 3.645A pdb=" N ARG B 166 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 195 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLU B 193 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR B 170 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 191 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 176 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AA9, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.210A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.210A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.226A pdb=" N LEU E 97 " --> pdb=" O PRO E 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 72 through 73 removed outlier: 3.994A pdb=" N HIS E 81 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 174 through 177 removed outlier: 6.268A pdb=" N PHE E 174 " --> pdb=" O THR E 261 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR E 263 " --> pdb=" O PHE E 174 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE E 176 " --> pdb=" O TYR E 263 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.498A pdb=" N THR E 184 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR E 225 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS E 186 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 278 through 283 Processing sheet with id=AB7, first strand: chain 'E' and resid 292 through 300 removed outlier: 7.053A pdb=" N VAL E 292 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU E 358 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA E 294 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 407 through 413 removed outlier: 6.132A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLU E 505 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 421 through 425 removed outlier: 6.711A pdb=" N LEU E 465 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS E 424 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY E 463 " --> pdb=" O LYS E 424 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 455 " --> pdb=" O ILE E 464 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AC2, first strand: chain 'E' and resid 589 through 591 Processing sheet with id=AC3, first strand: chain 'E' and resid 594 through 596 Processing sheet with id=AC4, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AC5, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.211A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.211A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.226A pdb=" N LEU F 97 " --> pdb=" O PRO F 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 72 through 73 removed outlier: 3.994A pdb=" N HIS F 81 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 174 through 177 removed outlier: 6.268A pdb=" N PHE F 174 " --> pdb=" O THR F 261 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR F 263 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE F 176 " --> pdb=" O TYR F 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.499A pdb=" N THR F 184 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR F 225 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS F 186 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 278 through 283 Processing sheet with id=AD4, first strand: chain 'F' and resid 292 through 300 removed outlier: 7.052A pdb=" N VAL F 292 " --> pdb=" O LEU F 358 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU F 358 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA F 294 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 407 through 413 removed outlier: 6.133A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLU F 505 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 421 through 425 removed outlier: 6.710A pdb=" N LEU F 465 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS F 424 " --> pdb=" O GLY F 463 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY F 463 " --> pdb=" O LYS F 424 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 455 " --> pdb=" O ILE F 464 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD8, first strand: chain 'F' and resid 589 through 591 Processing sheet with id=AD9, first strand: chain 'F' and resid 594 through 596 486 hydrogen bonds defined for protein. 1350 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: 4.65 Time building geometry restraints manager: 6.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5136 1.35 - 1.47: 3653 1.47 - 1.59: 6561 1.59 - 1.71: 0 1.71 - 1.84: 154 Bond restraints: 15504 Sorted by residual: bond pdb=" C1 NAG E2006 " pdb=" O5 NAG E2006 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C1 NAG F2006 " pdb=" O5 NAG F2006 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" C1 NAG E2008 " pdb=" O5 NAG E2008 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.79e+00 bond pdb=" C1 NAG F2008 " pdb=" O5 NAG F2008 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C1 NAG F2005 " pdb=" O5 NAG F2005 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 15499 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.91: 516 106.91 - 113.69: 8365 113.69 - 120.46: 5980 120.46 - 127.23: 5980 127.23 - 134.01: 155 Bond angle restraints: 20996 Sorted by residual: angle pdb=" N ASN E 579 " pdb=" CA ASN E 579 " pdb=" C ASN E 579 " ideal model delta sigma weight residual 114.64 107.57 7.07 1.52e+00 4.33e-01 2.16e+01 angle pdb=" N ASN F 579 " pdb=" CA ASN F 579 " pdb=" C ASN F 579 " ideal model delta sigma weight residual 114.64 107.58 7.06 1.52e+00 4.33e-01 2.16e+01 angle pdb=" C VAL F 303 " pdb=" N VAL F 304 " pdb=" CA VAL F 304 " ideal model delta sigma weight residual 122.13 128.77 -6.64 1.85e+00 2.92e-01 1.29e+01 angle pdb=" C VAL E 303 " pdb=" N VAL E 304 " pdb=" CA VAL E 304 " ideal model delta sigma weight residual 122.13 128.76 -6.63 1.85e+00 2.92e-01 1.28e+01 angle pdb=" CA TYR C 181 " pdb=" CB TYR C 181 " pdb=" CG TYR C 181 " ideal model delta sigma weight residual 113.90 120.12 -6.22 1.80e+00 3.09e-01 1.19e+01 ... (remaining 20991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 9353 16.11 - 32.22: 296 32.22 - 48.34: 58 48.34 - 64.45: 10 64.45 - 80.56: 10 Dihedral angle restraints: 9727 sinusoidal: 4173 harmonic: 5554 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 -166.56 80.56 1 1.00e+01 1.00e-02 8.03e+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 -166.54 80.54 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CB CYS E 515 " pdb=" SG CYS E 515 " pdb=" SG CYS E 531 " pdb=" CB CYS E 531 " ideal model delta sinusoidal sigma weight residual 93.00 168.71 -75.71 1 1.00e+01 1.00e-02 7.23e+01 ... (remaining 9724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1446 0.040 - 0.079: 625 0.079 - 0.119: 205 0.119 - 0.159: 46 0.159 - 0.199: 2 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CA ASP E 378 " pdb=" N ASP E 378 " pdb=" C ASP E 378 " pdb=" CB ASP E 378 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CA ASP F 378 " pdb=" N ASP F 378 " pdb=" C ASP F 378 " pdb=" CB ASP F 378 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA VAL E 425 " pdb=" N VAL E 425 " pdb=" C VAL E 425 " pdb=" CB VAL E 425 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 2321 not shown) Planarity restraints: 2762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 334 " 0.024 2.00e-02 2.50e+03 1.56e-02 6.05e+00 pdb=" CG TRP F 334 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP F 334 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP F 334 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP F 334 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 334 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 334 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 334 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 334 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 334 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 334 " -0.024 2.00e-02 2.50e+03 1.54e-02 5.91e+00 pdb=" CG TRP E 334 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP E 334 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP E 334 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 334 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 334 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 334 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 334 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 334 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 334 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 190 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO C 191 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 191 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 191 " -0.031 5.00e-02 4.00e+02 ... (remaining 2759 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 12 2.21 - 2.88: 5253 2.88 - 3.55: 18341 3.55 - 4.23: 32802 4.23 - 4.90: 55680 Nonbonded interactions: 112088 Sorted by model distance: nonbonded pdb=" OD2 ASP F 300 " pdb=" OH TYR F 314 " model vdw 1.534 2.440 nonbonded pdb=" OD2 ASP E 300 " pdb=" OH TYR E 314 " model vdw 1.534 2.440 nonbonded pdb=" OD1 ASP F 230 " pdb=" OE1 GLU F 232 " model vdw 1.615 3.040 nonbonded pdb=" OD1 ASP E 230 " pdb=" OE1 GLU E 232 " model vdw 1.615 3.040 nonbonded pdb=" OD1 ASP F 266 " pdb=" OD2 ASP F 302 " model vdw 1.689 3.040 ... (remaining 112083 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: 1.390 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: 5.530 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 39.990 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2309 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 : 0.004 0.051 15504 Z= 0.279 Angle : 0.785 9.523 20996 Z= 0.439 Chirality : 0.049 0.199 2324 Planarity : 0.006 0.056 2750 Dihedral : 8.536 74.283 5968 Min Nonbonded Distance : 1.534 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.12 % Allowed : 1.68 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.75 (0.16), residues: 1860 helix: -3.14 (0.14), residues: 454 sheet: -1.38 (0.22), residues: 490 loop : -2.77 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP F 334 HIS 0.004 0.001 HIS E 246 PHE 0.022 0.002 PHE F 188 TYR 0.020 0.002 TYR C 181 ARG 0.011 0.001 ARG E 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 368 time to evaluate : 1.679 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 221 PHE cc_start: 0.2945 (m-80) cc_final: 0.1656 (m-10) REVERT: E 264 ASP cc_start: 0.0252 (t0) cc_final: -0.0423 (t0) REVERT: E 291 THR cc_start: 0.5853 (m) cc_final: 0.5468 (m) REVERT: F 410 LEU cc_start: 0.3601 (pp) cc_final: 0.3384 (pt) outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.3531 time to fit residues: 175.6586 Evaluate side-chains 158 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 96 optimal weight: 0.2980 chunk 76 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS C 44 ASN C 250 ASN C 272 HIS C 274 ASN C 308 ASN E 103 HIS ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 246 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN D 225 GLN F 187 GLN F 246 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 GLN F 437 ASN F 482 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3082 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 15504 Z= 0.175 Angle : 0.589 7.764 20996 Z= 0.304 Chirality : 0.043 0.177 2324 Planarity : 0.005 0.053 2750 Dihedral : 5.412 55.369 2378 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.05 % Allowed : 9.27 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.43 (0.18), residues: 1860 helix: -1.03 (0.22), residues: 458 sheet: -0.89 (0.23), residues: 476 loop : -2.32 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 334 HIS 0.012 0.001 HIS E 114 PHE 0.014 0.001 PHE F 419 TYR 0.029 0.002 TYR C 181 ARG 0.005 0.001 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 1.764 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: E 264 ASP cc_start: 0.0396 (t0) cc_final: 0.0147 (t0) outliers start: 34 outliers final: 14 residues processed: 197 average time/residue: 0.3171 time to fit residues: 88.4405 Evaluate side-chains 140 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 536 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 169 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 160 HIS C 201 HIS C 250 ASN ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN C 357 ASN ** E 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 GLN D 274 ASN F 54 HIS F 103 HIS F 499 GLN ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4090 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15504 Z= 0.261 Angle : 0.688 10.128 20996 Z= 0.359 Chirality : 0.045 0.224 2324 Planarity : 0.006 0.110 2750 Dihedral : 5.426 56.079 2378 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 2.59 % Allowed : 9.75 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.94 (0.18), residues: 1860 helix: -0.34 (0.24), residues: 448 sheet: -0.73 (0.23), residues: 460 loop : -2.07 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 334 HIS 0.005 0.001 HIS F 71 PHE 0.018 0.002 PHE D 207 TYR 0.033 0.003 TYR E 204 ARG 0.011 0.001 ARG F 540 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 177 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 122 TYR cc_start: 0.3190 (p90) cc_final: 0.2895 (p90) REVERT: D 248 LYS cc_start: 0.4755 (OUTLIER) cc_final: 0.3829 (mttt) outliers start: 43 outliers final: 25 residues processed: 212 average time/residue: 0.3197 time to fit residues: 94.9331 Evaluate side-chains 146 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 319 LEU Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 536 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 88 optimal weight: 0.0030 chunk 18 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 114 optimal weight: 0.0570 chunk 171 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 overall best weight: 0.7110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4220 moved from start: 0.7228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 15504 Z= 0.158 Angle : 0.558 8.278 20996 Z= 0.284 Chirality : 0.042 0.332 2324 Planarity : 0.004 0.042 2750 Dihedral : 4.858 55.837 2378 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.17 % Allowed : 11.67 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.42 (0.19), residues: 1860 helix: 0.09 (0.25), residues: 456 sheet: -0.26 (0.25), residues: 436 loop : -1.82 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 334 HIS 0.007 0.001 HIS E 352 PHE 0.011 0.001 PHE F 466 TYR 0.022 0.002 TYR C 181 ARG 0.008 0.000 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 1.634 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: E 215 ARG cc_start: 0.2213 (OUTLIER) cc_final: -0.0508 (ptm-80) REVERT: E 484 MET cc_start: 0.2798 (tmm) cc_final: 0.1240 (ptm) outliers start: 36 outliers final: 23 residues processed: 181 average time/residue: 0.2766 time to fit residues: 74.4499 Evaluate side-chains 145 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 410 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 20.0000 chunk 103 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS C 44 ASN C 186 ASN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS F 343 ASN F 482 HIS F 499 GLN ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5355 moved from start: 1.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 15504 Z= 0.383 Angle : 0.882 10.636 20996 Z= 0.456 Chirality : 0.052 0.290 2324 Planarity : 0.007 0.071 2750 Dihedral : 6.382 85.710 2378 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.79 % Allowed : 12.58 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.33 (0.18), residues: 1860 helix: -1.07 (0.23), residues: 454 sheet: -0.89 (0.24), residues: 442 loop : -2.12 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 334 HIS 0.008 0.002 HIS D 201 PHE 0.022 0.002 PHE F 188 TYR 0.029 0.003 TYR F 36 ARG 0.013 0.001 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 195 time to evaluate : 1.747 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 186 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8388 (t0) REVERT: C 219 MET cc_start: 0.7642 (mtm) cc_final: 0.7440 (mtm) REVERT: E 215 ARG cc_start: 0.2841 (OUTLIER) cc_final: -0.0070 (ptm-80) REVERT: D 184 ILE cc_start: 0.8232 (mt) cc_final: 0.8030 (mt) REVERT: D 248 LYS cc_start: 0.5543 (OUTLIER) cc_final: 0.4686 (ptpt) REVERT: F 402 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.6014 (pp) outliers start: 63 outliers final: 39 residues processed: 243 average time/residue: 0.3010 time to fit residues: 103.5681 Evaluate side-chains 163 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 609 CYS Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 181 optimal weight: 0.0670 chunk 150 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 579 ASN D 201 HIS F 341 GLN F 482 HIS F 499 GLN ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5254 moved from start: 1.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 15504 Z= 0.187 Angle : 0.638 14.835 20996 Z= 0.324 Chirality : 0.043 0.189 2324 Planarity : 0.004 0.050 2750 Dihedral : 5.243 78.193 2378 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.41 % Allowed : 15.64 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.83 (0.19), residues: 1860 helix: -0.45 (0.24), residues: 445 sheet: -0.61 (0.25), residues: 406 loop : -1.85 (0.18), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 106 HIS 0.004 0.001 HIS E 352 PHE 0.015 0.001 PHE E 126 TYR 0.033 0.002 TYR D 217 ARG 0.009 0.001 ARG E 494 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8350 (t0) REVERT: C 300 MET cc_start: 0.8167 (mmm) cc_final: 0.7588 (mmm) REVERT: E 215 ARG cc_start: 0.2688 (OUTLIER) cc_final: 0.0217 (ptm-80) REVERT: D 184 ILE cc_start: 0.8160 (mt) cc_final: 0.7887 (mt) REVERT: D 248 LYS cc_start: 0.4879 (OUTLIER) cc_final: 0.4151 (ptpt) outliers start: 40 outliers final: 27 residues processed: 178 average time/residue: 0.2635 time to fit residues: 70.6753 Evaluate side-chains 142 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 609 CYS Chi-restraints excluded: chain E residue 611 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN C 169 ASN E 114 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 HIS F 499 GLN ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5569 moved from start: 1.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 15504 Z= 0.258 Angle : 0.698 20.098 20996 Z= 0.354 Chirality : 0.045 0.228 2324 Planarity : 0.006 0.101 2750 Dihedral : 5.403 78.482 2378 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.61 % Allowed : 14.92 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 (0.19), residues: 1860 helix: -0.56 (0.23), residues: 453 sheet: -0.72 (0.26), residues: 396 loop : -1.84 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 334 HIS 0.006 0.001 HIS E 443 PHE 0.014 0.002 PHE C 342 TYR 0.023 0.002 TYR D 243 ARG 0.010 0.001 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 151 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: C 300 MET cc_start: 0.8120 (mmm) cc_final: 0.7482 (mmm) REVERT: E 215 ARG cc_start: 0.3519 (OUTLIER) cc_final: 0.0686 (ptm-80) REVERT: E 567 ASP cc_start: 0.4992 (p0) cc_final: 0.4779 (p0) REVERT: D 172 ASP cc_start: 0.6594 (m-30) cc_final: 0.6170 (t0) REVERT: D 184 ILE cc_start: 0.8475 (mt) cc_final: 0.8218 (mt) REVERT: D 248 LYS cc_start: 0.5067 (OUTLIER) cc_final: 0.4147 (mttt) REVERT: F 484 MET cc_start: 0.4615 (tpt) cc_final: 0.4359 (tpt) REVERT: F 485 VAL cc_start: 0.6510 (OUTLIER) cc_final: 0.6306 (m) REVERT: F 562 THR cc_start: 0.8032 (t) cc_final: 0.7680 (m) outliers start: 60 outliers final: 37 residues processed: 195 average time/residue: 0.2889 time to fit residues: 82.1908 Evaluate side-chains 165 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 609 CYS Chi-restraints excluded: chain E residue 611 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 35 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 123 optimal weight: 0.0170 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 ASN C 169 ASN E 114 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 1.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15504 Z= 0.169 Angle : 0.621 11.428 20996 Z= 0.313 Chirality : 0.043 0.238 2324 Planarity : 0.004 0.038 2750 Dihedral : 4.993 78.404 2378 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.53 % Allowed : 16.43 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.58 (0.19), residues: 1860 helix: -0.12 (0.25), residues: 444 sheet: -0.69 (0.25), residues: 418 loop : -1.65 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 334 HIS 0.003 0.001 HIS F 392 PHE 0.042 0.001 PHE D 338 TYR 0.020 0.001 TYR A 183 ARG 0.005 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7153 (mm-30) REVERT: B 188 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: C 300 MET cc_start: 0.8085 (mmm) cc_final: 0.7535 (mmm) REVERT: E 215 ARG cc_start: 0.3305 (OUTLIER) cc_final: 0.0404 (ptm-80) REVERT: E 322 ASP cc_start: 0.2137 (t0) cc_final: 0.1767 (t70) REVERT: E 567 ASP cc_start: 0.4654 (p0) cc_final: 0.4386 (p0) REVERT: D 172 ASP cc_start: 0.6712 (m-30) cc_final: 0.6207 (t0) REVERT: D 248 LYS cc_start: 0.4932 (OUTLIER) cc_final: 0.4327 (ptpt) REVERT: F 562 THR cc_start: 0.7916 (t) cc_final: 0.7581 (m) outliers start: 42 outliers final: 28 residues processed: 182 average time/residue: 0.2824 time to fit residues: 75.3795 Evaluate side-chains 157 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 611 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 168 optimal weight: 0.0570 chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN C 235 GLN E 54 HIS E 114 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN F 333 HIS F 371 GLN F 403 HIS ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 1.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 15504 Z= 0.380 Angle : 0.882 14.469 20996 Z= 0.452 Chirality : 0.051 0.211 2324 Planarity : 0.006 0.065 2750 Dihedral : 6.444 72.432 2378 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.25 % Allowed : 15.94 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.27 (0.18), residues: 1860 helix: -1.03 (0.23), residues: 445 sheet: -1.08 (0.24), residues: 428 loop : -1.93 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 139 HIS 0.006 0.002 HIS A 184 PHE 0.041 0.003 PHE E 185 TYR 0.031 0.003 TYR D 181 ARG 0.009 0.001 ARG E 297 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 144 time to evaluate : 1.738 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 158 ARG cc_start: 0.5944 (tpm170) cc_final: 0.5430 (mmp-170) REVERT: B 188 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: C 235 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7566 (tp-100) REVERT: C 300 MET cc_start: 0.8154 (mmm) cc_final: 0.7575 (mmt) REVERT: E 88 ILE cc_start: 0.3243 (OUTLIER) cc_final: 0.2628 (pt) REVERT: E 215 ARG cc_start: 0.4233 (OUTLIER) cc_final: 0.0919 (ptm-80) REVERT: E 338 THR cc_start: 0.6896 (p) cc_final: 0.6696 (p) REVERT: D 206 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7927 (mm-40) REVERT: D 248 LYS cc_start: 0.5566 (OUTLIER) cc_final: 0.5044 (ptpt) REVERT: F 43 ASP cc_start: 0.4748 (m-30) cc_final: 0.4080 (t0) REVERT: F 402 LEU cc_start: 0.7005 (pp) cc_final: 0.5971 (mp) REVERT: F 562 THR cc_start: 0.8210 (t) cc_final: 0.7934 (m) outliers start: 54 outliers final: 35 residues processed: 183 average time/residue: 0.3028 time to fit residues: 79.3549 Evaluate side-chains 150 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 110 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 611 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 235 GLU Chi-restraints excluded: chain F residue 237 TYR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 30.0000 chunk 84 optimal weight: 0.3980 chunk 124 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 158 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 235 GLN E 114 HIS E 179 ASN E 333 HIS ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 moved from start: 1.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15504 Z= 0.201 Angle : 0.667 10.949 20996 Z= 0.340 Chirality : 0.045 0.211 2324 Planarity : 0.005 0.043 2750 Dihedral : 5.376 53.638 2378 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.11 % Allowed : 18.23 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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 (0.19), residues: 1860 helix: -0.36 (0.24), residues: 440 sheet: -1.01 (0.24), residues: 434 loop : -1.74 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 334 HIS 0.004 0.001 HIS F 443 PHE 0.039 0.002 PHE D 338 TYR 0.024 0.002 TYR D 181 ARG 0.010 0.001 ARG E 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 135 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 188 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: C 99 MET cc_start: 0.5714 (ptm) cc_final: 0.5417 (ptm) REVERT: C 300 MET cc_start: 0.8074 (mmm) cc_final: 0.7539 (mmt) REVERT: C 343 THR cc_start: 0.7650 (p) cc_final: 0.7416 (p) REVERT: E 88 ILE cc_start: 0.3236 (tp) cc_final: 0.2490 (pt) REVERT: E 215 ARG cc_start: 0.3684 (OUTLIER) cc_final: 0.1084 (ptm-80) REVERT: E 567 ASP cc_start: 0.4816 (p0) cc_final: 0.4530 (p0) REVERT: D 248 LYS cc_start: 0.5453 (OUTLIER) cc_final: 0.4453 (mttt) REVERT: F 562 THR cc_start: 0.7960 (t) cc_final: 0.7688 (m) outliers start: 35 outliers final: 24 residues processed: 157 average time/residue: 0.2660 time to fit residues: 63.1751 Evaluate side-chains 141 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 611 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 235 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 HIS E 187 GLN E 443 HIS ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN F 443 HIS ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.158128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.139346 restraints weight = 46982.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.138965 restraints weight = 54990.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.139944 restraints weight = 49807.025| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 1.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 15504 Z= 0.390 Angle : 0.859 13.151 20996 Z= 0.443 Chirality : 0.050 0.203 2324 Planarity : 0.006 0.053 2750 Dihedral : 6.412 59.402 2378 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.59 % Allowed : 17.39 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.44 (0.18), residues: 1860 helix: -1.00 (0.23), residues: 444 sheet: -1.32 (0.24), residues: 442 loop : -2.07 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 37 HIS 0.020 0.002 HIS E 103 PHE 0.025 0.003 PHE E 185 TYR 0.040 0.003 TYR D 181 ARG 0.012 0.001 ARG E 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2849.27 seconds wall clock time: 52 minutes 13.34 seconds (3133.34 seconds total)