Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 01:47:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/04_2023/7bym_30245_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/04_2023/7bym_30245.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/04_2023/7bym_30245_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/04_2023/7bym_30245_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/04_2023/7bym_30245_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/04_2023/7bym_30245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/04_2023/7bym_30245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/04_2023/7bym_30245_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/04_2023/7bym_30245_neut_updated.pdb" } resolution = 3.1 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= 0.002 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: 7 Type Number sf(0) Gaussians K 3 8.98 5 P 12 5.49 5 S 92 5.16 5 C 10548 2.51 5 N 2756 2.21 5 O 2996 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E GLU 551": "OE1" <-> "OE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G ARG 168": "NH1" <-> "NH2" Residue "G PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G GLU 551": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16411 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "C" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "E" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "G" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2872 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "B" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "D" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "F" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "H" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 81 Unusual residues: {' K': 3, 'FBX': 1, 'PT5': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'FBX': 1, 'PT5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'FBX': 1, 'PT5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'FBX': 1, 'PT5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PT5:plan-6': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.63, per 1000 atoms: 0.53 Number of scatterers: 16411 At special positions: 0 Unit cell: (135.875, 135.875, 123.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 3 19.00 S 92 16.00 P 12 15.00 F 4 9.00 O 2996 8.00 N 2756 7.00 C 10548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.86 Conformation dependent library (CDL) restraints added in 2.5 seconds 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 4 sheets defined 74.0% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 98 through 120 removed outlier: 4.654A pdb=" N VAL A 103 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER A 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 156 removed outlier: 3.536A pdb=" N ILE A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N CYS A 156 " --> pdb=" O TRP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 173 through 191 Processing helix chain 'A' and resid 200 through 217 removed outlier: 4.505A pdb=" N ARG A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN A 210 " --> pdb=" O MET A 206 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 214 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 235 through 260 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 294 through 311 removed outlier: 3.780A pdb=" N SER A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 335 removed outlier: 3.925A pdb=" N HIS A 334 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 removed outlier: 3.612A pdb=" N ILE A 346 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 351 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 354 " --> pdb=" O ARG A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 528 through 553 removed outlier: 4.183A pdb=" N LEU A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 586 Processing helix chain 'C' and resid 75 through 92 Processing helix chain 'C' and resid 98 through 120 removed outlier: 4.655A pdb=" N VAL C 103 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER C 111 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 156 removed outlier: 3.536A pdb=" N ILE C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY C 155 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N CYS C 156 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 170 Processing helix chain 'C' and resid 173 through 191 Processing helix chain 'C' and resid 200 through 217 removed outlier: 4.505A pdb=" N ARG C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE C 208 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN C 210 " --> pdb=" O MET C 206 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE C 211 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C 214 " --> pdb=" O GLN C 210 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 235 through 260 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.667A pdb=" N LEU C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 removed outlier: 4.029A pdb=" N HIS C 334 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE C 335 " --> pdb=" O ARG C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 356 removed outlier: 3.611A pdb=" N ILE C 346 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 351 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 354 " --> pdb=" O ARG C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 528 through 553 removed outlier: 4.294A pdb=" N LEU C 553 " --> pdb=" O PHE C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 586 Processing helix chain 'E' and resid 75 through 92 Processing helix chain 'E' and resid 98 through 120 removed outlier: 4.654A pdb=" N VAL E 103 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE E 110 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER E 111 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 156 removed outlier: 3.536A pdb=" N ILE E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY E 155 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N CYS E 156 " --> pdb=" O TRP E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 170 Processing helix chain 'E' and resid 173 through 191 Processing helix chain 'E' and resid 200 through 217 removed outlier: 4.505A pdb=" N ARG E 207 " --> pdb=" O LEU E 203 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE E 208 " --> pdb=" O ARG E 204 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU E 209 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN E 210 " --> pdb=" O MET E 206 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE E 211 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG E 213 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET E 214 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 235 through 260 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 294 through 311 removed outlier: 3.528A pdb=" N LEU E 306 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 310 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 335 removed outlier: 3.854A pdb=" N HIS E 334 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE E 335 " --> pdb=" O ARG E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 356 removed outlier: 3.612A pdb=" N ILE E 346 " --> pdb=" O ALA E 343 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG E 351 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 354 " --> pdb=" O ARG E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 361 No H-bonds generated for 'chain 'E' and resid 359 through 361' Processing helix chain 'E' and resid 528 through 553 removed outlier: 4.177A pdb=" N LEU E 553 " --> pdb=" O PHE E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 586 Processing helix chain 'G' and resid 75 through 92 Processing helix chain 'G' and resid 98 through 120 removed outlier: 4.654A pdb=" N VAL G 103 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE G 110 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER G 111 " --> pdb=" O LEU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 156 removed outlier: 3.536A pdb=" N ILE G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY G 155 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N CYS G 156 " --> pdb=" O TRP G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 170 Processing helix chain 'G' and resid 173 through 191 Processing helix chain 'G' and resid 200 through 217 removed outlier: 4.505A pdb=" N ARG G 207 " --> pdb=" O LEU G 203 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU G 209 " --> pdb=" O SER G 205 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN G 210 " --> pdb=" O MET G 206 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU G 212 " --> pdb=" O PHE G 208 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET G 214 " --> pdb=" O GLN G 210 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET G 217 " --> pdb=" O ARG G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 235 through 260 Processing helix chain 'G' and resid 270 through 281 Processing helix chain 'G' and resid 294 through 311 removed outlier: 3.551A pdb=" N LEU G 306 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER G 309 " --> pdb=" O LEU G 305 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE G 310 " --> pdb=" O LEU G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 335 removed outlier: 3.855A pdb=" N HIS G 334 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE G 335 " --> pdb=" O ARG G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 356 removed outlier: 3.611A pdb=" N ILE G 346 " --> pdb=" O ALA G 343 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG G 351 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER G 354 " --> pdb=" O ARG G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 528 through 553 removed outlier: 4.199A pdb=" N LEU G 553 " --> pdb=" O PHE G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 586 Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.605A pdb=" N PHE B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 38 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'D' and resid 6 through 19 removed outlier: 3.604A pdb=" N PHE D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'F' and resid 6 through 19 removed outlier: 3.604A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 45 through 54 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'F' and resid 118 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'H' and resid 6 through 19 removed outlier: 3.604A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 38 Processing helix chain 'H' and resid 45 through 54 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 79 through 92 removed outlier: 4.071A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'H' and resid 118 through 127 Processing helix chain 'H' and resid 138 through 145 Processing sheet with id= A, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= B, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= C, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= D, first strand: chain 'H' and resid 99 through 101 1029 hydrogen bonds defined for protein. 2739 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 7.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3132 1.33 - 1.45: 4387 1.45 - 1.58: 9049 1.58 - 1.71: 16 1.71 - 1.83: 160 Bond restraints: 16744 Sorted by residual: bond pdb=" C22 PT5 C 702 " pdb=" C23 PT5 C 702 " ideal model delta sigma weight residual 1.592 1.498 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C22 PT5 E 702 " pdb=" C23 PT5 E 702 " ideal model delta sigma weight residual 1.592 1.498 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C22 PT5 A 701 " pdb=" C23 PT5 A 701 " ideal model delta sigma weight residual 1.592 1.498 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C22 PT5 G 702 " pdb=" C23 PT5 G 702 " ideal model delta sigma weight residual 1.592 1.498 0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C10 PT5 G 702 " pdb=" O16 PT5 G 702 " ideal model delta sigma weight residual 1.432 1.342 0.090 2.00e-02 2.50e+03 2.04e+01 ... (remaining 16739 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.55: 297 106.55 - 113.53: 9198 113.53 - 120.52: 7344 120.52 - 127.50: 5608 127.50 - 134.49: 149 Bond angle restraints: 22596 Sorted by residual: angle pdb=" C18 PT5 C 702 " pdb=" C19 PT5 C 702 " pdb=" C20 PT5 C 702 " ideal model delta sigma weight residual 85.86 125.70 -39.84 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C18 PT5 E 702 " pdb=" C19 PT5 E 702 " pdb=" C20 PT5 E 702 " ideal model delta sigma weight residual 85.86 125.69 -39.83 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C18 PT5 A 701 " pdb=" C19 PT5 A 701 " pdb=" C20 PT5 A 701 " ideal model delta sigma weight residual 85.86 125.68 -39.82 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C18 PT5 G 702 " pdb=" C19 PT5 G 702 " pdb=" C20 PT5 G 702 " ideal model delta sigma weight residual 85.86 125.66 -39.80 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C21 PT5 E 702 " pdb=" C22 PT5 E 702 " pdb=" C23 PT5 E 702 " ideal model delta sigma weight residual 152.70 125.65 27.05 3.00e+00 1.11e-01 8.13e+01 ... (remaining 22591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.53: 9345 34.53 - 69.05: 410 69.05 - 103.58: 36 103.58 - 138.10: 5 138.10 - 172.63: 8 Dihedral angle restraints: 9804 sinusoidal: 4016 harmonic: 5788 Sorted by residual: dihedral pdb=" C12 PT5 E 702 " pdb=" C13 PT5 E 702 " pdb=" C14 PT5 E 702 " pdb=" C15 PT5 E 702 " ideal model delta sinusoidal sigma weight residual 21.27 -166.10 -172.63 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C12 PT5 G 702 " pdb=" C13 PT5 G 702 " pdb=" C14 PT5 G 702 " pdb=" C15 PT5 G 702 " ideal model delta sinusoidal sigma weight residual 21.27 -166.18 -172.55 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C12 PT5 A 701 " pdb=" C13 PT5 A 701 " pdb=" C14 PT5 A 701 " pdb=" C15 PT5 A 701 " ideal model delta sinusoidal sigma weight residual 21.27 -166.60 -172.13 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 9801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1785 0.045 - 0.090: 509 0.090 - 0.135: 125 0.135 - 0.181: 49 0.181 - 0.226: 20 Chirality restraints: 2488 Sorted by residual: chirality pdb=" CA VAL G 583 " pdb=" N VAL G 583 " pdb=" C VAL G 583 " pdb=" CB VAL G 583 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL A 583 " pdb=" N VAL A 583 " pdb=" C VAL A 583 " pdb=" CB VAL A 583 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA VAL C 583 " pdb=" N VAL C 583 " pdb=" C VAL C 583 " pdb=" CB VAL C 583 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2485 not shown) Planarity restraints: 2832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 PT5 E 702 " 0.254 2.00e-02 2.50e+03 2.54e-01 6.44e+02 pdb=" C18 PT5 E 702 " -0.256 2.00e-02 2.50e+03 pdb=" C19 PT5 E 702 " -0.251 2.00e-02 2.50e+03 pdb=" C20 PT5 E 702 " 0.253 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 PT5 G 702 " 0.252 2.00e-02 2.50e+03 2.50e-01 6.26e+02 pdb=" C18 PT5 G 702 " -0.255 2.00e-02 2.50e+03 pdb=" C19 PT5 G 702 " -0.245 2.00e-02 2.50e+03 pdb=" C20 PT5 G 702 " 0.249 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 PT5 A 701 " -0.243 2.00e-02 2.50e+03 2.42e-01 5.88e+02 pdb=" C18 PT5 A 701 " 0.245 2.00e-02 2.50e+03 pdb=" C19 PT5 A 701 " 0.240 2.00e-02 2.50e+03 pdb=" C20 PT5 A 701 " -0.242 2.00e-02 2.50e+03 ... (remaining 2829 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.63: 198 2.63 - 3.25: 17899 3.25 - 3.88: 32070 3.88 - 4.51: 41981 4.51 - 5.14: 64541 Nonbonded interactions: 156689 Sorted by model distance: nonbonded pdb=" NH2 ARG A 95 " pdb=" O ASP B 95 " model vdw 1.997 2.520 nonbonded pdb=" NH2 ARG G 95 " pdb=" O ASP H 95 " model vdw 2.030 2.520 nonbonded pdb=" O THR C 282 " pdb=" OG1 THR C 283 " model vdw 2.052 2.440 nonbonded pdb=" O THR A 282 " pdb=" OG1 THR A 283 " model vdw 2.052 2.440 nonbonded pdb=" O THR G 282 " pdb=" OG1 THR G 283 " model vdw 2.052 2.440 ... (remaining 156684 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' and resid 74 through 588) selection = (chain 'C' and resid 74 through 588) selection = (chain 'E' and resid 74 through 588) selection = (chain 'G' and resid 74 through 588) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.200 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 42.280 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4692 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 : 0.009 0.094 16744 Z= 0.624 Angle : 1.241 39.844 22596 Z= 0.679 Chirality : 0.051 0.226 2488 Planarity : 0.013 0.254 2832 Dihedral : 19.112 172.631 6068 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.42 % Favored : 98.37 % Rotamer Outliers : 8.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.17), residues: 1968 helix: -0.17 (0.12), residues: 1484 sheet: None (None), residues: 0 loop : 0.18 (0.27), residues: 484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 270 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 147 outliers final: 80 residues processed: 385 average time/residue: 0.2972 time to fit residues: 166.8665 Evaluate side-chains 258 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 178 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.2037 time to fit residues: 29.2174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 177 optimal weight: 0.1980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 125 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN C 234 HIS C 329 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN E 569 HIS ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN B 111 ASN D 137 ASN H 41 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4818 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 16744 Z= 0.257 Angle : 0.599 13.718 22596 Z= 0.305 Chirality : 0.039 0.184 2488 Planarity : 0.004 0.038 2832 Dihedral : 11.630 172.408 2300 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 0.81 % Favored : 98.98 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.19), residues: 1968 helix: 1.39 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : 1.32 (0.30), residues: 484 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 192 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 27 residues processed: 236 average time/residue: 0.2723 time to fit residues: 98.6897 Evaluate side-chains 182 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1559 time to fit residues: 10.4155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 158 optimal weight: 0.3980 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 124 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4872 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 16744 Z= 0.272 Angle : 0.589 11.736 22596 Z= 0.297 Chirality : 0.038 0.152 2488 Planarity : 0.003 0.029 2832 Dihedral : 10.535 170.546 2300 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.42 % Favored : 98.37 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.19), residues: 1968 helix: 1.75 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : 1.30 (0.30), residues: 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 173 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 208 average time/residue: 0.2832 time to fit residues: 89.1912 Evaluate side-chains 180 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1647 time to fit residues: 10.1081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4828 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 16744 Z= 0.165 Angle : 0.534 12.526 22596 Z= 0.266 Chirality : 0.035 0.155 2488 Planarity : 0.003 0.027 2832 Dihedral : 9.630 142.021 2300 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.27 % Favored : 98.53 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.19), residues: 1968 helix: 1.96 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : 1.58 (0.30), residues: 484 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 204 average time/residue: 0.2805 time to fit residues: 87.2640 Evaluate side-chains 183 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 174 time to evaluate : 1.923 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1971 time to fit residues: 5.7031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 0.0870 chunk 47 optimal weight: 7.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 HIS ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4831 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 16744 Z= 0.163 Angle : 0.527 12.041 22596 Z= 0.262 Chirality : 0.035 0.140 2488 Planarity : 0.003 0.027 2832 Dihedral : 8.906 131.068 2300 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 0.97 % Favored : 98.83 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.19), residues: 1968 helix: 2.09 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : 1.26 (0.30), residues: 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 177 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 18 residues processed: 189 average time/residue: 0.2520 time to fit residues: 74.3490 Evaluate side-chains 182 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 1.672 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1485 time to fit residues: 7.3278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 chunk 157 optimal weight: 0.0670 chunk 87 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4826 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 16744 Z= 0.158 Angle : 0.521 11.976 22596 Z= 0.257 Chirality : 0.034 0.138 2488 Planarity : 0.003 0.027 2832 Dihedral : 8.505 120.886 2300 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.02 % Favored : 98.83 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.19), residues: 1968 helix: 2.17 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : 1.25 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 189 average time/residue: 0.2787 time to fit residues: 81.6240 Evaluate side-chains 182 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 1.918 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1667 time to fit residues: 6.5079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 159 optimal weight: 0.4980 chunk 105 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4844 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16744 Z= 0.166 Angle : 0.525 12.008 22596 Z= 0.260 Chirality : 0.034 0.132 2488 Planarity : 0.003 0.025 2832 Dihedral : 8.168 116.980 2300 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.17 % Favored : 98.68 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.19), residues: 1968 helix: 2.17 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : 1.26 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 187 average time/residue: 0.2632 time to fit residues: 76.5322 Evaluate side-chains 172 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1456 time to fit residues: 4.7567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.3980 chunk 75 optimal weight: 0.0470 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.0770 chunk 36 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN E 564 GLN ** G 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4813 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 16744 Z= 0.141 Angle : 0.522 12.152 22596 Z= 0.255 Chirality : 0.034 0.130 2488 Planarity : 0.003 0.024 2832 Dihedral : 7.869 113.001 2300 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 0.91 % Favored : 98.93 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.19), residues: 1968 helix: 2.23 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : 1.21 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 188 average time/residue: 0.2546 time to fit residues: 76.3979 Evaluate side-chains 176 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1562 time to fit residues: 4.1514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 165 optimal weight: 0.4980 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 0.1980 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN ** G 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4880 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16744 Z= 0.222 Angle : 0.557 11.865 22596 Z= 0.277 Chirality : 0.035 0.129 2488 Planarity : 0.003 0.039 2832 Dihedral : 7.858 114.899 2300 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.27 % Favored : 98.63 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.19), residues: 1968 helix: 2.12 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : 1.18 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 160 average time/residue: 0.2538 time to fit residues: 65.6602 Evaluate side-chains 156 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1592 time to fit residues: 3.4069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.0670 chunk 186 optimal weight: 4.9990 chunk 113 optimal weight: 0.0570 chunk 88 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 195 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 564 GLN ** G 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4822 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 16744 Z= 0.146 Angle : 0.533 12.165 22596 Z= 0.259 Chirality : 0.034 0.127 2488 Planarity : 0.003 0.030 2832 Dihedral : 7.629 112.203 2300 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 0.91 % Favored : 98.98 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.19), residues: 1968 helix: 2.16 (0.14), residues: 1492 sheet: None (None), residues: 0 loop : 1.26 (0.29), residues: 476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 167 average time/residue: 0.2559 time to fit residues: 68.0485 Evaluate side-chains 161 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1454 time to fit residues: 3.1486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 47 optimal weight: 0.0050 chunk 143 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.0030 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 85 ASN ** G 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.225267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126734 restraints weight = 23513.598| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.57 r_work: 0.3274 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 16744 Z= 0.155 Angle : 0.527 12.094 22596 Z= 0.259 Chirality : 0.034 0.126 2488 Planarity : 0.003 0.033 2832 Dihedral : 7.564 111.683 2300 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.17 % Favored : 98.73 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.19), residues: 1968 helix: 2.17 (0.14), residues: 1492 sheet: None (None), residues: 0 loop : 1.26 (0.29), residues: 476 =============================================================================== Job complete usr+sys time: 3535.46 seconds wall clock time: 64 minutes 43.15 seconds (3883.15 seconds total)