Starting phenix.real_space_refine on Sat Mar 16 00:04:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2n_20575/03_2024/6q2n_20575_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2n_20575/03_2024/6q2n_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_20575/03_2024/6q2n_20575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2n_20575/03_2024/6q2n_20575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2n_20575/03_2024/6q2n_20575_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2n_20575/03_2024/6q2n_20575_neut.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 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. 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-5265/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: 7.09, per 1000 atoms: 0.54 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: 4.90 Conformation dependent library (CDL) restraints added in 2.3 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: 1.33 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: 3.86 Time building geometry restraints manager: 5.32 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 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: 0.640 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: 3.100 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 35.510 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 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 % Allowed : 2.30 % Favored : 97.02 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP F 139 HIS 0.010 0.002 HIS B 203 PHE 0.026 0.004 PHE B 142 TYR 0.028 0.005 TYR D 174 ARG 0.023 0.002 ARG C 171 *********************** 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 : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PRO cc_start: 0.7509 (Cg_endo) cc_final: 0.7265 (Cg_exo) REVERT: E 73 TYR cc_start: 0.6775 (m-10) cc_final: 0.5451 (m-10) REVERT: E 122 TYR cc_start: 0.5348 (p90) cc_final: 0.4906 (p90) REVERT: E 153 SER cc_start: 0.8798 (m) cc_final: 0.8352 (t) REVERT: D 200 PHE cc_start: 0.7511 (m-80) cc_final: 0.6562 (m-80) REVERT: F 73 TYR cc_start: 0.6790 (m-10) cc_final: 0.5442 (m-10) REVERT: F 122 TYR cc_start: 0.5410 (p90) cc_final: 0.4869 (p90) REVERT: F 136 GLU cc_start: 0.2480 (tt0) cc_final: 0.2220 (mm-30) REVERT: F 153 SER cc_start: 0.8827 (m) cc_final: 0.8393 (t) REVERT: F 357 VAL cc_start: 0.7855 (t) cc_final: 0.7647 (p) outliers start: 10 outliers final: 6 residues processed: 320 average time/residue: 0.2924 time to fit residues: 128.2745 Evaluate side-chains 155 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.8980 chunk 96 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 443 HIS B 124 HIS D 153 ASN D 162 ASN ** 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 443 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13406 Z= 0.178 Angle : 0.733 9.869 18172 Z= 0.376 Chirality : 0.045 0.159 2034 Planarity : 0.005 0.045 2362 Dihedral : 6.565 27.546 1822 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.99 % Favored : 92.94 % Rotamer: Outliers : 0.41 % Allowed : 3.25 % Favored : 96.34 % 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: -3.17 (0.19), residues: 1630 helix: -1.36 (0.26), residues: 312 sheet: -1.42 (0.27), residues: 366 loop : -2.76 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 139 HIS 0.011 0.001 HIS B 198 PHE 0.017 0.002 PHE C 331 TYR 0.024 0.002 TYR C 301 ARG 0.008 0.001 ARG E 360 *********************** 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 224 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 218 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PRO cc_start: 0.7558 (Cg_endo) cc_final: 0.7267 (Cg_exo) REVERT: C 230 VAL cc_start: 0.6322 (t) cc_final: 0.6087 (t) REVERT: C 297 MET cc_start: 0.6432 (mmm) cc_final: 0.5980 (mmm) REVERT: E 73 TYR cc_start: 0.6619 (m-10) cc_final: 0.5587 (m-10) REVERT: E 289 GLU cc_start: 0.8590 (tp30) cc_final: 0.8114 (tp30) REVERT: E 290 ASP cc_start: 0.7189 (m-30) cc_final: 0.6973 (m-30) REVERT: E 466 PHE cc_start: 0.5035 (p90) cc_final: 0.4810 (p90) REVERT: B 125 LEU cc_start: 0.6562 (mt) cc_final: 0.6336 (mt) REVERT: B 155 THR cc_start: 0.7275 (m) cc_final: 0.6732 (m) REVERT: B 178 CYS cc_start: 0.1679 (OUTLIER) cc_final: 0.1406 (t) REVERT: D 200 PHE cc_start: 0.7113 (m-80) cc_final: 0.6908 (m-80) REVERT: F 73 TYR cc_start: 0.6451 (m-10) cc_final: 0.5211 (m-10) REVERT: F 289 GLU cc_start: 0.8595 (tp30) cc_final: 0.8125 (tp30) REVERT: F 290 ASP cc_start: 0.7116 (m-30) cc_final: 0.6906 (m-30) REVERT: F 466 PHE cc_start: 0.5070 (p90) cc_final: 0.4848 (p90) outliers start: 6 outliers final: 2 residues processed: 224 average time/residue: 0.2787 time to fit residues: 86.8332 Evaluate side-chains 134 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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: 10.9990 chunk 46 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 134 optimal weight: 0.0980 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- 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 C 347 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** B 176 GLN D 153 ASN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 340 ASN D 347 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13406 Z= 0.274 Angle : 0.786 10.360 18172 Z= 0.398 Chirality : 0.047 0.254 2034 Planarity : 0.005 0.056 2362 Dihedral : 6.532 29.387 1822 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 0.34 % Allowed : 4.27 % Favored : 95.39 % 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: -2.97 (0.19), residues: 1630 helix: -1.15 (0.25), residues: 340 sheet: -1.36 (0.28), residues: 352 loop : -2.64 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 334 HIS 0.013 0.002 HIS E 81 PHE 0.042 0.002 PHE D 264 TYR 0.033 0.002 TYR D 254 ARG 0.009 0.001 ARG D 225 *********************** 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 179 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 174 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.6015 (tp) cc_final: 0.5281 (tp) REVERT: A 158 LYS cc_start: 0.8040 (tttt) cc_final: 0.7636 (mmmt) REVERT: A 181 PRO cc_start: 0.7811 (Cg_endo) cc_final: 0.7534 (Cg_exo) REVERT: E 73 TYR cc_start: 0.6974 (m-10) cc_final: 0.6297 (m-10) REVERT: E 289 GLU cc_start: 0.8423 (tp30) cc_final: 0.7951 (tp30) REVERT: B 125 LEU cc_start: 0.6535 (mt) cc_final: 0.6297 (mt) REVERT: D 297 MET cc_start: 0.6564 (mmm) cc_final: 0.6278 (mmm) REVERT: F 289 GLU cc_start: 0.8506 (tp30) cc_final: 0.8035 (tp30) outliers start: 5 outliers final: 2 residues processed: 177 average time/residue: 0.2577 time to fit residues: 64.5757 Evaluate side-chains 131 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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: 10.0000 chunk 113 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 81 HIS ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN E 186 HIS E 187 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 HIS D 153 ASN D 253 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN F 81 HIS ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS 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: 0.5691 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 13406 Z= 0.253 Angle : 0.750 11.805 18172 Z= 0.382 Chirality : 0.047 0.354 2034 Planarity : 0.005 0.055 2362 Dihedral : 6.276 25.171 1822 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.14 % Allowed : 3.05 % Favored : 96.82 % 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: -2.94 (0.19), residues: 1630 helix: -1.07 (0.26), residues: 328 sheet: -1.52 (0.27), residues: 370 loop : -2.55 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 312 HIS 0.008 0.001 HIS B 203 PHE 0.024 0.002 PHE D 264 TYR 0.029 0.002 TYR D 301 ARG 0.006 0.000 ARG D 225 *********************** 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 168 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.6271 (tp) cc_final: 0.5496 (tp) REVERT: A 158 LYS cc_start: 0.8051 (tttt) cc_final: 0.7568 (mmmt) REVERT: A 181 PRO cc_start: 0.7859 (Cg_endo) cc_final: 0.7565 (Cg_exo) REVERT: E 73 TYR cc_start: 0.6953 (m-10) cc_final: 0.6383 (m-10) REVERT: E 289 GLU cc_start: 0.8494 (tp30) cc_final: 0.7958 (tp30) REVERT: D 297 MET cc_start: 0.6550 (mmm) cc_final: 0.6209 (mmm) REVERT: F 73 TYR cc_start: 0.6945 (m-10) cc_final: 0.6452 (m-10) REVERT: F 289 GLU cc_start: 0.8536 (tp30) cc_final: 0.8048 (tp30) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.2829 time to fit residues: 65.9441 Evaluate side-chains 132 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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: 50.0000 chunk 91 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 119 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 144 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 overall best weight: 4.5786 ------------------------------------------------------------------------------- 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 187 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 13406 Z= 0.306 Angle : 0.785 17.013 18172 Z= 0.402 Chirality : 0.048 0.362 2034 Planarity : 0.005 0.060 2362 Dihedral : 6.406 32.165 1822 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.17 % Favored : 88.77 % Rotamer: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % 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: -3.08 (0.19), residues: 1630 helix: -1.20 (0.25), residues: 328 sheet: -1.62 (0.27), residues: 378 loop : -2.64 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 334 HIS 0.007 0.001 HIS D 207 PHE 0.030 0.002 PHE D 264 TYR 0.023 0.002 TYR B 197 ARG 0.005 0.001 ARG D 225 *********************** 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 170 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8174 (tttt) cc_final: 0.7676 (mmmt) REVERT: A 181 PRO cc_start: 0.8065 (Cg_endo) cc_final: 0.7755 (Cg_exo) REVERT: E 175 ARG cc_start: 0.6868 (ttm110) cc_final: 0.6668 (ptm160) REVERT: E 289 GLU cc_start: 0.8353 (tp30) cc_final: 0.8021 (tp30) REVERT: B 125 LEU cc_start: 0.6160 (mt) cc_final: 0.5863 (mt) REVERT: D 297 MET cc_start: 0.6636 (mmm) cc_final: 0.6229 (mmm) REVERT: F 289 GLU cc_start: 0.8396 (tp30) cc_final: 0.8042 (tp30) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.2815 time to fit residues: 67.5055 Evaluate side-chains 138 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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: 4.9990 chunk 144 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 39 optimal weight: 30.0000 chunk 160 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 54 HIS ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 13406 Z= 0.209 Angle : 0.714 18.637 18172 Z= 0.360 Chirality : 0.046 0.315 2034 Planarity : 0.005 0.052 2362 Dihedral : 5.967 34.278 1822 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: -0.94 (0.26), residues: 328 sheet: -1.62 (0.27), residues: 374 loop : -2.54 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 85 HIS 0.005 0.001 HIS A 198 PHE 0.030 0.002 PHE F 393 TYR 0.017 0.002 TYR D 301 ARG 0.005 0.000 ARG D 225 *********************** 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 173 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PRO cc_start: 0.8041 (Cg_endo) cc_final: 0.7727 (Cg_exo) REVERT: E 289 GLU cc_start: 0.8364 (tp30) cc_final: 0.7783 (tp30) REVERT: E 290 ASP cc_start: 0.7371 (m-30) cc_final: 0.7105 (m-30) REVERT: D 297 MET cc_start: 0.6634 (mmm) cc_final: 0.6182 (mmm) REVERT: F 289 GLU cc_start: 0.8402 (tp30) cc_final: 0.7848 (tp30) REVERT: F 290 ASP cc_start: 0.7234 (m-30) cc_final: 0.7023 (m-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2762 time to fit residues: 67.3494 Evaluate side-chains 134 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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: 6.9990 chunk 91 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 159 optimal weight: 0.0870 chunk 100 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- 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** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 13406 Z= 0.241 Angle : 0.741 18.756 18172 Z= 0.373 Chirality : 0.046 0.294 2034 Planarity : 0.005 0.073 2362 Dihedral : 5.952 34.256 1822 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.43 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -2.86 (0.19), residues: 1630 helix: -0.86 (0.26), residues: 328 sheet: -1.54 (0.27), residues: 382 loop : -2.53 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 334 HIS 0.005 0.001 HIS A 124 PHE 0.018 0.002 PHE D 264 TYR 0.026 0.002 TYR B 197 ARG 0.005 0.000 ARG C 225 *********************** 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 167 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PRO cc_start: 0.8020 (Cg_endo) cc_final: 0.7703 (Cg_exo) REVERT: C 296 VAL cc_start: 0.7884 (m) cc_final: 0.7562 (p) REVERT: C 297 MET cc_start: 0.7114 (tpt) cc_final: 0.6821 (tpt) REVERT: E 289 GLU cc_start: 0.8308 (tp30) cc_final: 0.8006 (tp30) REVERT: E 617 LYS cc_start: 0.7012 (ttmt) cc_final: 0.6490 (tttt) REVERT: D 297 MET cc_start: 0.6766 (mmm) cc_final: 0.6296 (mmm) REVERT: F 289 GLU cc_start: 0.8337 (tp30) cc_final: 0.8014 (tp30) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2562 time to fit residues: 61.7209 Evaluate side-chains 128 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.436 ------------------------------------------------------------------------------- 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: 0.9990 chunk 95 optimal weight: 8.9990 chunk 48 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN ** 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** ** B 203 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 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 13406 Z= 0.268 Angle : 0.757 18.141 18172 Z= 0.384 Chirality : 0.047 0.320 2034 Planarity : 0.005 0.066 2362 Dihedral : 6.175 35.728 1822 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.12 % Favored : 89.82 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -2.89 (0.19), residues: 1630 helix: -0.95 (0.26), residues: 328 sheet: -1.55 (0.26), residues: 394 loop : -2.53 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 334 HIS 0.010 0.001 HIS E 114 PHE 0.020 0.002 PHE D 264 TYR 0.034 0.002 TYR B 197 ARG 0.005 0.000 ARG D 225 *********************** 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 165 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PRO cc_start: 0.8119 (Cg_endo) cc_final: 0.7869 (Cg_exo) REVERT: C 317 ASN cc_start: 0.8056 (m110) cc_final: 0.7416 (t0) REVERT: E 289 GLU cc_start: 0.8396 (tp30) cc_final: 0.8053 (tp30) REVERT: D 174 TYR cc_start: 0.5403 (p90) cc_final: 0.5134 (p90) REVERT: F 289 GLU cc_start: 0.8384 (tp30) cc_final: 0.8043 (tp30) REVERT: F 617 LYS cc_start: 0.6875 (ttmt) cc_final: 0.6471 (tttt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2500 time to fit residues: 60.0759 Evaluate side-chains 130 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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: 3.9990 chunk 149 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 13406 Z= 0.257 Angle : 0.752 18.074 18172 Z= 0.380 Chirality : 0.046 0.275 2034 Planarity : 0.005 0.076 2362 Dihedral : 6.048 33.555 1822 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -2.82 (0.19), residues: 1630 helix: -0.88 (0.26), residues: 328 sheet: -1.49 (0.26), residues: 390 loop : -2.49 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 334 HIS 0.005 0.001 HIS B 203 PHE 0.020 0.002 PHE B 142 TYR 0.029 0.002 TYR B 197 ARG 0.004 0.000 ARG C 171 *********************** 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 168 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PRO cc_start: 0.8153 (Cg_endo) cc_final: 0.7895 (Cg_exo) REVERT: C 317 ASN cc_start: 0.8120 (m110) cc_final: 0.7483 (t0) REVERT: E 289 GLU cc_start: 0.8331 (tp30) cc_final: 0.8022 (tp30) REVERT: E 525 ARG cc_start: 0.4471 (ttt90) cc_final: 0.3301 (ttp80) REVERT: D 297 MET cc_start: 0.6811 (mmm) cc_final: 0.6464 (mmm) REVERT: F 289 GLU cc_start: 0.8386 (tp30) cc_final: 0.8045 (tp30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2598 time to fit residues: 63.0936 Evaluate side-chains 126 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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: 2.9990 chunk 74 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 131 optimal weight: 50.0000 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 ASN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5795 moved from start: 0.5516 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= 0.253 Angle : 0.746 18.027 18172 Z= 0.378 Chirality : 0.047 0.262 2034 Planarity : 0.006 0.077 2362 Dihedral : 6.029 32.498 1822 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -2.79 (0.20), residues: 1630 helix: -0.80 (0.26), residues: 334 sheet: -1.48 (0.26), residues: 390 loop : -2.50 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 334 HIS 0.005 0.001 HIS B 203 PHE 0.024 0.002 PHE A 142 TYR 0.029 0.002 TYR B 197 ARG 0.004 0.000 ARG C 171 ********************** 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 168 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 PRO cc_start: 0.8215 (Cg_endo) cc_final: 0.7940 (Cg_exo) REVERT: C 297 MET cc_start: 0.6353 (mmm) cc_final: 0.5828 (mmm) REVERT: C 317 ASN cc_start: 0.8043 (m110) cc_final: 0.7505 (t0) REVERT: E 289 GLU cc_start: 0.8382 (tp30) cc_final: 0.8059 (tp30) REVERT: E 525 ARG cc_start: 0.4524 (ttt90) cc_final: 0.3126 (ttp80) REVERT: F 122 TYR cc_start: 0.4950 (p90) cc_final: 0.4538 (p90) REVERT: F 289 GLU cc_start: 0.8459 (tp30) cc_final: 0.8095 (tp30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2466 time to fit residues: 61.6075 Evaluate side-chains 132 residues out of total 1486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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: 7.9990 chunk 40 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 0.0670 chunk 131 optimal weight: 50.0000 chunk 55 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- 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** ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN ** B 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.154647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.135567 restraints weight = 48215.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.137614 restraints weight = 33457.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.139032 restraints weight = 25125.933| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13406 Z= 0.305 Angle : 0.798 17.551 18172 Z= 0.406 Chirality : 0.048 0.266 2034 Planarity : 0.006 0.089 2362 Dihedral : 6.327 34.052 1822 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.09 % Favored : 87.85 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -2.96 (0.19), residues: 1630 helix: -1.16 (0.25), residues: 334 sheet: -1.58 (0.27), residues: 380 loop : -2.51 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 334 HIS 0.005 0.001 HIS D 207 PHE 0.022 0.002 PHE D 264 TYR 0.031 0.003 TYR B 197 ARG 0.005 0.000 ARG B 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2488.90 seconds wall clock time: 45 minutes 51.78 seconds (2751.78 seconds total)