Starting phenix.real_space_refine (version: dev) on Mon Feb 20 21:36:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2n_20575/02_2023/6q2n_20575_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2n_20575/02_2023/6q2n_20575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2n_20575/02_2023/6q2n_20575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2n_20575/02_2023/6q2n_20575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2n_20575/02_2023/6q2n_20575_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2n_20575/02_2023/6q2n_20575_neut.pdb" } resolution = 4.4 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13140 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 659 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1554 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 192} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4353 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 518} Chain breaks: 8 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 659 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1554 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 192} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 4353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4353 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 518} Chain breaks: 8 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.87, per 1000 atoms: 0.60 Number of scatterers: 13140 At special positions: 0 Unit cell: (127.33, 210.79, 75.97, 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 116 16.00 O 2486 8.00 N 2302 7.00 C 8228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 179 " distance=2.02 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 208 " distance=2.02 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 210 " distance=2.04 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS B 178 " distance=2.10 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 167 " distance=2.04 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 192 " distance=2.01 Simple disulfide: pdb=" SG CYS C 187 " - pdb=" SG CYS C 233 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 313 " distance=2.03 Simple disulfide: pdb=" SG CYS C 250 " - pdb=" SG CYS C 256 " distance=2.04 Simple disulfide: pdb=" SG CYS C 267 " - pdb=" SG CYS C 285 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 325 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 142 " distance=2.02 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS E 515 " - pdb=" SG CYS E 531 " distance=2.02 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=2.01 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=2.01 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 179 " distance=2.02 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 208 " distance=2.02 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 210 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 167 " distance=2.04 Simple disulfide: pdb=" SG CYS D 178 " - pdb=" SG CYS D 192 " distance=2.01 Simple disulfide: pdb=" SG CYS D 187 " - pdb=" SG CYS D 233 " distance=2.03 Simple disulfide: pdb=" SG CYS D 216 " - pdb=" SG CYS D 221 " distance=2.04 Simple disulfide: pdb=" SG CYS D 243 " - pdb=" SG CYS D 313 " distance=2.03 Simple disulfide: pdb=" SG CYS D 250 " - pdb=" SG CYS D 256 " distance=2.03 Simple disulfide: pdb=" SG CYS D 267 " - pdb=" SG CYS D 285 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 315 " - pdb=" SG CYS D 325 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 142 " distance=2.02 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS F 515 " - pdb=" SG CYS F 531 " distance=2.02 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=2.01 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=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.77 Conformation dependent library (CDL) restraints added in 2.1 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 36 sheets defined 24.3% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'C' and resid 152 through 164 removed outlier: 3.649A pdb=" N ASP C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.516A pdb=" N CYS C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 4.199A pdb=" N SER C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 227 removed outlier: 3.533A pdb=" N THR C 222 " --> pdb=" O ASP C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 235 Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.724A pdb=" N CYS C 267 " --> pdb=" O PHE C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 321 through 334 removed outlier: 3.923A pdb=" N PHE C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 Processing helix chain 'E' and resid 102 through 111 removed outlier: 3.766A pdb=" N VAL E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 160 removed outlier: 3.746A pdb=" N LEU E 160 " --> pdb=" O CYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 167 removed outlier: 4.025A pdb=" N CYS E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 162 through 167' Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.787A pdb=" N ARG E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.785A pdb=" N ALA E 432 " --> pdb=" O ASN E 429 " (cutoff:3.500A) removed outlier: 4.401A 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 524 through 530 Processing helix chain 'E' and resid 564 through 568 removed outlier: 4.213A pdb=" N ASP E 567 " --> pdb=" O THR E 564 " (cutoff:3.500A) removed outlier: 4.521A 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 'B' and resid 154 through 164 Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.650A pdb=" N ASP D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 188 through 203 removed outlier: 3.515A pdb=" N CYS D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 removed outlier: 4.198A pdb=" N SER D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 removed outlier: 3.533A pdb=" N THR D 222 " --> pdb=" O ASP D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 235 Processing helix chain 'D' and resid 242 through 252 Processing helix chain 'D' and resid 253 through 267 removed outlier: 3.725A pdb=" N CYS D 267 " --> pdb=" O PHE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 290 Processing helix chain 'D' and resid 321 through 334 removed outlier: 3.924A pdb=" N PHE D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 Processing helix chain 'F' and resid 102 through 111 removed outlier: 3.767A pdb=" N VAL F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 160 removed outlier: 3.746A pdb=" N LEU F 160 " --> pdb=" O CYS F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 4.024A pdb=" N CYS F 166 " --> pdb=" O PRO F 162 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 162 through 167' Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.788A pdb=" N ARG F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.785A pdb=" N ALA F 432 " --> pdb=" O ASN F 429 " (cutoff:3.500A) removed outlier: 4.401A 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 524 through 530 Processing helix chain 'F' and resid 564 through 568 removed outlier: 4.213A pdb=" N ASP F 567 " --> pdb=" O THR F 564 " (cutoff:3.500A) removed outlier: 4.521A 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 sheet with id=AA1, first strand: chain 'A' and resid 119 through 126 Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA4, first strand: chain 'C' and resid 300 through 301 Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.383A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 39 through 42 removed outlier: 4.644A pdb=" N VAL E 42 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR E 152 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 71 through 73 removed outlier: 4.249A pdb=" N HIS E 81 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'E' and resid 174 through 176 removed outlier: 3.508A pdb=" N VAL E 256 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 241 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR E 237 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.035A pdb=" N THR E 184 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR E 225 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS E 186 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 280 through 283 removed outlier: 3.711A pdb=" N ALA E 281 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER E 396 " --> pdb=" O ALA E 281 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA E 373 " --> pdb=" O LEU E 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 292 through 298 removed outlier: 6.296A pdb=" N LEU E 356 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR E 295 " --> pdb=" O TYR E 354 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR E 354 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG E 297 " --> pdb=" O HIS E 352 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS E 352 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP E 353 " --> pdb=" O TRP E 334 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP E 334 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 407 through 412 removed outlier: 6.870A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS E 482 " --> pdb=" O SER E 445 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 424 through 425 removed outlier: 3.760A pdb=" N SER E 462 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE E 464 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL E 455 " --> pdb=" O ILE E 464 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AB8, first strand: chain 'E' and resid 594 through 596 Processing sheet with id=AB9, first strand: chain 'E' and resid 608 through 612 Processing sheet with id=AC1, first strand: chain 'B' and resid 119 through 126 Processing sheet with id=AC2, first strand: chain 'B' and resid 180 through 181 Processing sheet with id=AC3, first strand: chain 'B' and resid 190 through 191 Processing sheet with id=AC4, first strand: chain 'D' and resid 300 through 301 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: 6.381A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 39 through 42 removed outlier: 4.643A pdb=" N VAL F 42 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR F 152 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 71 through 73 removed outlier: 6.699A pdb=" N LEU F 72 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 86 through 89 Processing sheet with id=AD1, first strand: chain 'F' and resid 174 through 176 removed outlier: 3.508A pdb=" N VAL F 256 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR F 237 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.035A pdb=" N THR F 184 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR F 225 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS F 186 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 280 through 283 removed outlier: 3.711A pdb=" N ALA F 281 " --> pdb=" O ASN F 394 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER F 396 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA F 373 " --> pdb=" O LEU F 319 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 292 through 298 removed outlier: 6.296A pdb=" N LEU F 356 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR F 295 " --> pdb=" O TYR F 354 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR F 354 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG F 297 " --> pdb=" O HIS F 352 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS F 352 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP F 353 " --> pdb=" O TRP F 334 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP F 334 " --> pdb=" O ASP F 353 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 407 through 412 removed outlier: 6.870A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS F 482 " --> pdb=" O SER F 445 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 424 through 425 removed outlier: 3.760A pdb=" N SER F 462 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE F 464 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 4.142A 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 594 through 596 Processing sheet with id=AD9, first strand: chain 'F' and resid 608 through 612 402 hydrogen bonds defined for protein. 1098 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: 3.72 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4351 1.34 - 1.47: 3239 1.47 - 1.60: 5690 1.60 - 1.72: 0 1.72 - 1.85: 126 Bond restraints: 13406 Sorted by residual: bond pdb=" CA ASN F 113 " pdb=" C ASN F 113 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.41e+01 bond pdb=" CA ASN E 113 " pdb=" C ASN E 113 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.38e+01 bond pdb=" C THR C 298 " pdb=" N PRO C 299 " ideal model delta sigma weight residual 1.329 1.294 0.036 1.25e-02 6.40e+03 8.21e+00 bond pdb=" C THR D 298 " pdb=" N PRO D 299 " ideal model delta sigma weight residual 1.329 1.294 0.035 1.25e-02 6.40e+03 7.81e+00 bond pdb=" C GLN F 583 " pdb=" N ASP F 584 " ideal model delta sigma weight residual 1.333 1.295 0.038 1.47e-02 4.63e+03 6.63e+00 ... (remaining 13401 not shown) Histogram of bond angle deviations from ideal: 98.12 - 106.80: 463 106.80 - 115.48: 8070 115.48 - 124.16: 9254 124.16 - 132.83: 359 132.83 - 141.51: 26 Bond angle restraints: 18172 Sorted by residual: angle pdb=" C ARG E 112 " pdb=" N ASN E 113 " pdb=" CA ASN E 113 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C ARG F 112 " pdb=" N ASN F 113 " pdb=" CA ASN F 113 " ideal model delta sigma weight residual 121.54 131.23 -9.69 1.91e+00 2.74e-01 2.58e+01 angle pdb=" C TYR F 76 " pdb=" N ARG F 77 " pdb=" CA ARG F 77 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C TYR E 76 " pdb=" N ARG E 77 " pdb=" CA ARG E 77 " ideal model delta sigma weight residual 121.54 129.62 -8.08 1.91e+00 2.74e-01 1.79e+01 angle pdb=" N GLU A 153 " pdb=" CA GLU A 153 " pdb=" C GLU A 153 " ideal model delta sigma weight residual 110.80 119.10 -8.30 2.13e+00 2.20e-01 1.52e+01 ... (remaining 18167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7826 17.65 - 35.30: 347 35.30 - 52.94: 43 52.94 - 70.59: 0 70.59 - 88.24: 9 Dihedral angle restraints: 8225 sinusoidal: 3335 harmonic: 4890 Sorted by residual: dihedral pdb=" CB CYS A 178 " pdb=" SG CYS A 178 " pdb=" SG CYS B 178 " pdb=" CB CYS B 178 " ideal model delta sinusoidal sigma weight residual 93.00 -178.76 -88.24 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CB CYS F 515 " pdb=" SG CYS F 515 " pdb=" SG CYS F 531 " pdb=" CB CYS F 531 " ideal model delta sinusoidal sigma weight residual 93.00 172.88 -79.88 1 1.00e+01 1.00e-02 7.91e+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 93.00 172.87 -79.87 1 1.00e+01 1.00e-02 7.91e+01 ... (remaining 8222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1407 0.060 - 0.120: 493 0.120 - 0.180: 119 0.180 - 0.240: 11 0.240 - 0.300: 4 Chirality restraints: 2034 Sorted by residual: chirality pdb=" CA GLU B 153 " pdb=" N GLU B 153 " pdb=" C GLU B 153 " pdb=" CB GLU B 153 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA GLU A 153 " pdb=" N GLU A 153 " pdb=" C GLU A 153 " pdb=" CB GLU A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CG LEU D 155 " pdb=" CB LEU D 155 " pdb=" CD1 LEU D 155 " pdb=" CD2 LEU D 155 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2031 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 230 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.15e+00 pdb=" C VAL C 230 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL C 230 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO C 231 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 230 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.04e+00 pdb=" C VAL D 230 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL D 230 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO D 231 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 286 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.84e+00 pdb=" C LEU C 286 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU C 286 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU C 287 " 0.015 2.00e-02 2.50e+03 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 18 2.14 - 2.83: 4093 2.83 - 3.52: 16799 3.52 - 4.21: 30146 4.21 - 4.90: 49236 Nonbonded interactions: 100292 Sorted by model distance: nonbonded pdb=" OD1 ASP E 567 " pdb=" OD2 ASP E 584 " model vdw 1.449 3.040 nonbonded pdb=" OD1 ASP F 567 " pdb=" OD2 ASP F 584 " model vdw 1.449 3.040 nonbonded pdb=" OD2 ASP E 300 " pdb=" OD2 ASP E 378 " model vdw 1.490 3.040 nonbonded pdb=" OD2 ASP F 300 " pdb=" OD2 ASP F 378 " model vdw 1.491 3.040 nonbonded pdb=" OD1 ASP F 266 " pdb=" OD2 ASP F 302 " model vdw 1.605 3.040 ... (remaining 100287 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 116 5.16 5 C 8228 2.51 5 N 2302 2.21 5 O 2486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 3.650 Check model and map are aligned: 0.180 Process input model: 36.460 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 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 : 0.008 0.082 13406 Z= 0.500 Angle : 1.237 20.703 18172 Z= 0.687 Chirality : 0.063 0.300 2034 Planarity : 0.008 0.059 2362 Dihedral : 9.781 78.043 4896 Min Nonbonded Distance : 1.449 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.57 % Favored : 90.18 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.25 (0.17), residues: 1630 helix: -3.05 (0.19), residues: 326 sheet: -2.08 (0.26), residues: 376 loop : -3.16 (0.17), residues: 928 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 311 time to evaluate : 1.647 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: 10 outliers final: 6 residues processed: 320 average time/residue: 0.3018 time to fit residues: 132.1932 Evaluate side-chains 150 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1270 time to fit residues: 3.5382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 67 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 50 optimal weight: 0.2980 chunk 79 optimal weight: 0.4980 chunk 96 optimal weight: 8.9990 chunk 150 optimal weight: 20.0000 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 162 ASN C 207 HIS ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 340 ASN E 81 HIS ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 246 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 ASN E 403 HIS E 421 GLN E 443 HIS B 124 HIS D 153 ASN D 162 ASN D 207 HIS ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 340 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN F 246 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN F 403 HIS F 421 GLN F 443 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5536 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 13406 Z= 0.203 Angle : 0.755 10.480 18172 Z= 0.388 Chirality : 0.045 0.144 2034 Planarity : 0.006 0.068 2362 Dihedral : 6.746 28.227 1822 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -3.30 (0.18), residues: 1630 helix: -1.46 (0.25), residues: 312 sheet: -1.61 (0.26), residues: 378 loop : -2.80 (0.17), residues: 940 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 222 average time/residue: 0.2936 time to fit residues: 90.6879 Evaluate side-chains 134 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1167 time to fit residues: 2.7109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 125 optimal weight: 0.1980 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 163 optimal weight: 0.0670 chunk 134 optimal weight: 3.9990 chunk 149 optimal weight: 0.0020 chunk 51 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.6530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN E 81 HIS ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5529 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 13406 Z= 0.186 Angle : 0.703 9.473 18172 Z= 0.355 Chirality : 0.045 0.274 2034 Planarity : 0.005 0.054 2362 Dihedral : 6.170 29.047 1822 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -2.86 (0.19), residues: 1630 helix: -0.80 (0.27), residues: 316 sheet: -1.39 (0.28), residues: 358 loop : -2.60 (0.18), residues: 956 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.2891 time to fit residues: 74.0640 Evaluate side-chains 133 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN C 347 ASN E 81 HIS ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN E 187 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN D 253 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN D 347 ASN F 81 HIS ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.109 13406 Z= 0.318 Angle : 0.799 12.389 18172 Z= 0.408 Chirality : 0.048 0.361 2034 Planarity : 0.006 0.065 2362 Dihedral : 6.405 26.808 1822 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -2.98 (0.19), residues: 1630 helix: -1.17 (0.25), residues: 340 sheet: -1.53 (0.27), residues: 356 loop : -2.56 (0.18), residues: 934 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.3036 time to fit residues: 69.2848 Evaluate side-chains 122 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN E 54 HIS ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN D 253 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 13406 Z= 0.246 Angle : 0.727 17.375 18172 Z= 0.370 Chirality : 0.046 0.344 2034 Planarity : 0.005 0.054 2362 Dihedral : 6.142 30.521 1822 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.92 (0.19), residues: 1630 helix: -0.96 (0.26), residues: 328 sheet: -1.67 (0.26), residues: 388 loop : -2.50 (0.19), residues: 914 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2989 time to fit residues: 67.5788 Evaluate side-chains 128 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.4980 chunk 144 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 0.4980 chunk 39 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 133 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5742 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 13406 Z= 0.269 Angle : 0.750 18.705 18172 Z= 0.380 Chirality : 0.046 0.319 2034 Planarity : 0.005 0.056 2362 Dihedral : 6.131 34.803 1822 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.88 (0.19), residues: 1630 helix: -0.80 (0.26), residues: 318 sheet: -1.64 (0.26), residues: 388 loop : -2.51 (0.19), residues: 924 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.2827 time to fit residues: 67.1956 Evaluate side-chains 130 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.692 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5682 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 13406 Z= 0.223 Angle : 0.728 18.732 18172 Z= 0.366 Chirality : 0.046 0.288 2034 Planarity : 0.005 0.072 2362 Dihedral : 5.855 33.842 1822 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.74 (0.20), residues: 1630 helix: -0.58 (0.27), residues: 316 sheet: -1.53 (0.27), residues: 388 loop : -2.47 (0.19), residues: 926 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2725 time to fit residues: 64.4374 Evaluate side-chains 129 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.734 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 101 optimal weight: 0.0270 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5663 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 13406 Z= 0.218 Angle : 0.726 18.324 18172 Z= 0.365 Chirality : 0.046 0.280 2034 Planarity : 0.005 0.075 2362 Dihedral : 5.852 34.172 1822 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.65 (0.20), residues: 1630 helix: -0.61 (0.27), residues: 336 sheet: -1.43 (0.27), residues: 388 loop : -2.43 (0.19), residues: 906 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2713 time to fit residues: 65.1013 Evaluate side-chains 125 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 30.0000 chunk 139 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5713 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 13406 Z= 0.242 Angle : 0.744 18.208 18172 Z= 0.372 Chirality : 0.046 0.269 2034 Planarity : 0.005 0.065 2362 Dihedral : 5.804 34.103 1822 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.20), residues: 1630 helix: -0.65 (0.27), residues: 330 sheet: -1.43 (0.27), residues: 388 loop : -2.43 (0.19), residues: 912 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2453 time to fit residues: 54.6557 Evaluate side-chains 121 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.642 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 ASN ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 13406 Z= 0.210 Angle : 0.714 17.916 18172 Z= 0.357 Chirality : 0.045 0.251 2034 Planarity : 0.005 0.059 2362 Dihedral : 5.654 31.184 1822 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.53 (0.20), residues: 1630 helix: -0.47 (0.27), residues: 330 sheet: -1.37 (0.27), residues: 388 loop : -2.35 (0.19), residues: 912 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2327 time to fit residues: 53.1753 Evaluate side-chains 119 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.498 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 50.0000 chunk 55 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 GLN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.159100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.140179 restraints weight = 47819.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.142359 restraints weight = 32434.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.143939 restraints weight = 23949.257| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5758 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 13406 Z= 0.248 Angle : 0.745 17.521 18172 Z= 0.373 Chirality : 0.046 0.253 2034 Planarity : 0.005 0.059 2362 Dihedral : 5.715 31.395 1822 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.20), residues: 1630 helix: -0.58 (0.27), residues: 332 sheet: -1.32 (0.27), residues: 384 loop : -2.36 (0.19), residues: 914 =============================================================================== Job complete usr+sys time: 2424.53 seconds wall clock time: 44 minutes 49.36 seconds (2689.36 seconds total)