Starting phenix.real_space_refine (version: dev) on Fri May 13 22:59:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/05_2022/6q2o_20576_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/05_2022/6q2o_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_20576/05_2022/6q2o_20576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/05_2022/6q2o_20576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/05_2022/6q2o_20576_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/05_2022/6q2o_20576_neut.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 33, 'TRANS': 537, 'PCIS': 1} 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: {'PTRANS': 33, 'TRANS': 537, 'PCIS': 1} 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 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 chiralities: 6 Time building chain proxies: 8.39, per 1000 atoms: 0.55 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: 5.95 Conformation dependent library (CDL) restraints added in 2.5 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: 0.97 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: 4.61 Time building geometry restraints manager: 6.25 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=" CA ASP E 378 " pdb=" CB ASP E 378 " ideal model delta sigma weight residual 1.528 1.580 -0.051 2.61e-02 1.47e+03 3.88e+00 bond pdb=" CA ASP F 378 " pdb=" CB ASP F 378 " ideal model delta sigma weight residual 1.528 1.579 -0.051 2.61e-02 1.47e+03 3.78e+00 bond pdb=" C CYS F 565 " pdb=" N PRO F 566 " ideal model delta sigma weight residual 1.340 1.390 -0.050 2.76e-02 1.31e+03 3.24e+00 bond pdb=" C CYS E 565 " pdb=" N PRO E 566 " ideal model delta sigma weight residual 1.340 1.390 -0.050 2.76e-02 1.31e+03 3.22e+00 bond pdb=" C VAL E 304 " pdb=" N PRO E 305 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.58e+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: 9203 16.11 - 32.22: 272 32.22 - 48.34: 56 48.34 - 64.45: 6 64.45 - 80.56: 10 Dihedral angle restraints: 9547 sinusoidal: 3993 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 9544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1467 0.040 - 0.079: 616 0.079 - 0.119: 193 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 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. 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.090 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.130 Process input model: 39.990 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2303 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= 0.258 Angle : 0.772 9.523 20996 Z= 0.436 Chirality : 0.048 0.199 2324 Planarity : 0.006 0.056 2750 Dihedral : 8.383 74.283 5788 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 % 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 *********************** 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 : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.3406 time to fit residues: 170.7396 Evaluate side-chains 148 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5574 ------------------------------------------------------------------------------- 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: 0.5980 chunk 142 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 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: 6.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 104 GLN 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 421 GLN F 437 ASN F 482 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3013 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.106 15504 Z= 0.216 Angle : 0.642 13.366 20996 Z= 0.333 Chirality : 0.042 0.170 2324 Planarity : 0.006 0.093 2750 Dihedral : 4.901 42.424 2198 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 2.11 % 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: -2.42 (0.18), residues: 1860 helix: -1.00 (0.22), residues: 458 sheet: -0.90 (0.23), residues: 476 loop : -2.33 (0.18), residues: 926 *********************** 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 209 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 197 average time/residue: 0.3053 time to fit residues: 85.8971 Evaluate side-chains 136 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.777 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.1552 time to fit residues: 7.3719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 116 optimal weight: 0.2980 chunk 47 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 137 optimal weight: 10.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS B 187 HIS C 44 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS C 201 HIS ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN C 357 ASN E 44 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 GLN ** E 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS D 274 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS F 187 GLN F 443 HIS ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4850 moved from start: 0.9050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.230 15504 Z= 0.457 Angle : 1.019 13.307 20996 Z= 0.540 Chirality : 0.055 0.347 2324 Planarity : 0.009 0.129 2750 Dihedral : 6.682 75.235 2198 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.37 % Favored : 92.47 % Rotamer Outliers : 2.95 % 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: -2.82 (0.17), residues: 1860 helix: -1.56 (0.22), residues: 460 sheet: -1.00 (0.23), residues: 446 loop : -2.50 (0.18), residues: 954 *********************** 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 273 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 224 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 26 residues processed: 259 average time/residue: 0.2940 time to fit residues: 109.0807 Evaluate side-chains 156 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.826 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.1394 time to fit residues: 9.3672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 HIS C 186 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 HIS C 308 ASN ** 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 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 576 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5099 moved from start: 0.9722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 1.025 15504 Z= 0.675 Angle : 1.247 106.100 20996 Z= 0.586 Chirality : 0.053 0.310 2324 Planarity : 0.009 0.113 2750 Dihedral : 6.557 76.137 2198 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.58 % Favored : 92.37 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.11 % 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: -2.96 (0.17), residues: 1860 helix: -1.57 (0.22), residues: 446 sheet: -1.05 (0.24), residues: 422 loop : -2.63 (0.17), residues: 992 *********************** 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 185 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 135 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 26 residues processed: 171 average time/residue: 0.2834 time to fit residues: 71.4111 Evaluate side-chains 142 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1562 time to fit residues: 9.3414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN E 187 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 579 ASN E 610 ASN D 272 HIS F 341 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 1.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.171 15504 Z= 0.334 Angle : 0.804 17.066 20996 Z= 0.425 Chirality : 0.047 0.241 2324 Planarity : 0.007 0.114 2750 Dihedral : 5.944 85.879 2198 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 2.47 % 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: -2.54 (0.18), residues: 1860 helix: -1.14 (0.23), residues: 431 sheet: -0.90 (0.25), residues: 398 loop : -2.32 (0.17), residues: 1031 *********************** 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 216 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 19 residues processed: 198 average time/residue: 0.2573 time to fit residues: 77.1819 Evaluate side-chains 136 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1296 time to fit residues: 7.1473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS ** E 333 HIS ** 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: 0.5525 moved from start: 1.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.933 15504 Z= 0.561 Angle : 1.147 106.100 20996 Z= 0.528 Chirality : 0.049 0.515 2324 Planarity : 0.008 0.113 2750 Dihedral : 6.006 86.871 2198 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.06 % 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: -2.50 (0.18), residues: 1860 helix: -1.04 (0.24), residues: 431 sheet: -0.85 (0.26), residues: 394 loop : -2.32 (0.17), residues: 1035 *********************** 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 146 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 139 average time/residue: 0.2507 time to fit residues: 53.9653 Evaluate side-chains 126 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.813 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1342 time to fit residues: 6.1001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 83 optimal weight: 0.0030 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS ** E 333 HIS ** 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: 0.5524 moved from start: 1.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.945 15504 Z= 0.597 Angle : 1.225 106.100 20996 Z= 0.572 Chirality : 0.048 0.481 2324 Planarity : 0.008 0.156 2750 Dihedral : 6.026 86.763 2198 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.67 % Favored : 93.28 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.06 % 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: -2.47 (0.18), residues: 1860 helix: -0.98 (0.24), residues: 431 sheet: -0.85 (0.26), residues: 394 loop : -2.33 (0.17), residues: 1035 *********************** 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 129 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 124 average time/residue: 0.2480 time to fit residues: 48.5777 Evaluate side-chains 122 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1368 time to fit residues: 6.3993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 HIS E 179 ASN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 1.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.173 15504 Z= 0.296 Angle : 0.745 24.535 20996 Z= 0.389 Chirality : 0.046 0.280 2324 Planarity : 0.006 0.140 2750 Dihedral : 5.581 82.366 2198 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.72 % Favored : 93.23 % Rotamer Outliers : 1.02 % 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: -2.20 (0.18), residues: 1860 helix: -0.66 (0.25), residues: 427 sheet: -0.85 (0.25), residues: 400 loop : -2.12 (0.18), residues: 1033 *********************** 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 154 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 149 average time/residue: 0.3000 time to fit residues: 65.6023 Evaluate side-chains 108 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1955 time to fit residues: 3.9706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.0270 chunk 158 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 HIS E 333 HIS F 333 HIS F 576 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5593 moved from start: 1.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.193 15504 Z= 0.216 Angle : 0.691 14.546 20996 Z= 0.362 Chirality : 0.044 0.233 2324 Planarity : 0.006 0.175 2750 Dihedral : 4.971 60.418 2198 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.60 % 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: -0.25 (0.25), residues: 429 sheet: -0.77 (0.24), residues: 432 loop : -1.88 (0.19), residues: 999 *********************** 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 131 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 127 average time/residue: 0.3016 time to fit residues: 58.9365 Evaluate side-chains 107 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.877 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1579 time to fit residues: 4.1737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.0870 chunk 84 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 172 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 HIS F 333 HIS F 482 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5595 moved from start: 1.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.713 15504 Z= 0.278 Angle : 0.763 42.128 20996 Z= 0.421 Chirality : 0.043 0.239 2324 Planarity : 0.007 0.142 2750 Dihedral : 4.743 44.566 2198 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.06 % 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: -1.61 (0.19), residues: 1860 helix: -0.04 (0.25), residues: 431 sheet: -0.59 (0.25), residues: 412 loop : -1.76 (0.19), residues: 1017 ********************** 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 118 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 117 average time/residue: 0.2860 time to fit residues: 50.6692 Evaluate side-chains 102 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.821 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 62 optimal weight: 30.0000 chunk 153 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN C 186 ASN ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS E 114 HIS ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS F 482 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.165628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.147114 restraints weight = 47778.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.145471 restraints weight = 51270.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.146548 restraints weight = 44201.940| |-----------------------------------------------------------------------------| r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 1.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.871 15504 Z= 0.747 Angle : 1.060 51.803 20996 Z= 0.556 Chirality : 0.048 0.331 2324 Planarity : 0.008 0.184 2750 Dihedral : 5.219 42.240 2198 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.11 % 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: -1.91 (0.19), residues: 1860 helix: -0.47 (0.25), residues: 427 sheet: -0.69 (0.24), residues: 454 loop : -1.94 (0.19), residues: 979 =============================================================================== Job complete usr+sys time: 2556.33 seconds wall clock time: 47 minutes 39.51 seconds (2859.51 seconds total)