Starting phenix.real_space_refine on Fri Feb 16 20:38:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/02_2024/7bym_30245_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/02_2024/7bym_30245.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/02_2024/7bym_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_30245/02_2024/7bym_30245_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/02_2024/7bym_30245_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/02_2024/7bym_30245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/02_2024/7bym_30245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/02_2024/7bym_30245_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bym_30245/02_2024/7bym_30245_neut_updated.pdb" } resolution = 3.1 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= 0.002 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.99, per 1000 atoms: 0.55 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: 6.83 Conformation dependent library (CDL) restraints added in 2.9 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: 2.67 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: 4.31 Time building geometry restraints manager: 7.28 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: 9353 34.53 - 69.05: 421 69.05 - 103.58: 45 103.58 - 138.10: 9 138.10 - 172.63: 8 Dihedral angle restraints: 9836 sinusoidal: 4048 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 9833 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: 2.280 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: 7.940 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 44.820 Find NCS groups from input model: 1.120 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.430 ------------------------------------------------------------------------------- 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 : 19.737 172.631 6100 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 % Allowed : 17.57 % Favored : 73.76 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 350 HIS 0.013 0.002 HIS E 569 PHE 0.010 0.001 PHE D 68 TYR 0.079 0.004 TYR E 565 ARG 0.008 0.001 ARG A 351 *********************** 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 : 1.779 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 REVERT: A 137 PHE cc_start: 0.6715 (t80) cc_final: 0.6496 (t80) REVERT: A 178 ASP cc_start: 0.8371 (t70) cc_final: 0.8136 (t70) REVERT: A 217 MET cc_start: 0.8408 (mtt) cc_final: 0.6536 (tmm) REVERT: C 148 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.7023 (tt) REVERT: C 217 MET cc_start: 0.8161 (mtt) cc_final: 0.5875 (tmm) REVERT: E 217 MET cc_start: 0.8483 (mtt) cc_final: 0.6620 (tmm) REVERT: G 92 GLU cc_start: 0.6691 (tp30) cc_final: 0.6430 (mm-30) REVERT: G 137 PHE cc_start: 0.6697 (t80) cc_final: 0.6308 (t80) REVERT: G 178 ASP cc_start: 0.8188 (t70) cc_final: 0.7766 (t0) REVERT: G 214 MET cc_start: 0.8504 (mtp) cc_final: 0.8289 (mtp) REVERT: G 217 MET cc_start: 0.8387 (mtt) cc_final: 0.6548 (tmm) outliers start: 147 outliers final: 80 residues processed: 385 average time/residue: 0.3178 time to fit residues: 180.2321 Evaluate side-chains 262 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 181 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 TRP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 554 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain E residue 554 ARG Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 97 TRP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 333 LYS Chi-restraints excluded: chain G residue 554 ARG Chi-restraints excluded: chain G residue 558 VAL 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: 0.2980 chunk 50 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN D 137 ASN H 41 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4764 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16744 Z= 0.177 Angle : 0.564 13.704 22596 Z= 0.287 Chirality : 0.038 0.196 2488 Planarity : 0.004 0.037 2832 Dihedral : 15.299 166.322 2481 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 0.66 % Favored : 99.14 % Rotamer: Outliers : 3.42 % Allowed : 21.23 % Favored : 75.35 % 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: 2.11 (0.19), residues: 1968 helix: 1.52 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : 1.34 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 350 HIS 0.003 0.001 HIS G 124 PHE 0.013 0.001 PHE E 137 TYR 0.012 0.001 TYR C 80 ARG 0.006 0.000 ARG C 93 *********************** 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 264 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 206 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ASP cc_start: 0.8242 (t70) cc_final: 0.8038 (t70) REVERT: A 217 MET cc_start: 0.8302 (mtt) cc_final: 0.6524 (tmm) REVERT: C 203 LEU cc_start: 0.7715 (mp) cc_final: 0.7389 (mp) REVERT: C 217 MET cc_start: 0.8359 (mtt) cc_final: 0.6196 (tmm) REVERT: E 123 GLU cc_start: 0.7389 (mp0) cc_final: 0.7176 (mp0) REVERT: E 217 MET cc_start: 0.8474 (mtt) cc_final: 0.6621 (ptt) REVERT: E 272 ASP cc_start: 0.8405 (m-30) cc_final: 0.8123 (m-30) REVERT: G 92 GLU cc_start: 0.6694 (tp30) cc_final: 0.6378 (mm-30) REVERT: G 139 MET cc_start: 0.6456 (ttm) cc_final: 0.6088 (tpp) REVERT: G 217 MET cc_start: 0.8271 (mtt) cc_final: 0.6379 (tmm) REVERT: B 71 MET cc_start: 0.1061 (ttp) cc_final: 0.0731 (ttp) REVERT: D 76 MET cc_start: 0.2038 (mpp) cc_final: 0.1399 (mpp) REVERT: F 71 MET cc_start: 0.0933 (ttp) cc_final: 0.0551 (ttp) REVERT: F 76 MET cc_start: 0.2628 (mpp) cc_final: 0.1348 (mmt) REVERT: H 76 MET cc_start: 0.2172 (mpp) cc_final: 0.1679 (mpp) outliers start: 58 outliers final: 34 residues processed: 247 average time/residue: 0.2767 time to fit residues: 104.9116 Evaluate side-chains 200 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain C residue 97 TRP Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain G residue 97 TRP Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 156 CYS Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 334 HIS Chi-restraints excluded: chain G residue 335 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain H residue 136 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 176 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 85 ASN E 334 HIS ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4799 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16744 Z= 0.172 Angle : 0.538 11.912 22596 Z= 0.269 Chirality : 0.036 0.148 2488 Planarity : 0.003 0.027 2832 Dihedral : 13.117 153.989 2355 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 0.81 % Favored : 98.98 % Rotamer: Outliers : 3.54 % Allowed : 21.17 % Favored : 75.29 % 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: 2.69 (0.19), residues: 1968 helix: 2.00 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : 1.35 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 294 HIS 0.004 0.001 HIS A 124 PHE 0.018 0.001 PHE A 143 TYR 0.019 0.001 TYR E 353 ARG 0.004 0.000 ARG A 339 *********************** 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 241 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 181 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.8049 (OUTLIER) cc_final: 0.6958 (m-90) REVERT: A 217 MET cc_start: 0.8444 (mtt) cc_final: 0.6521 (tmm) REVERT: C 97 TRP cc_start: 0.7916 (OUTLIER) cc_final: 0.7573 (m-90) REVERT: C 217 MET cc_start: 0.8557 (mtt) cc_final: 0.6277 (tmm) REVERT: C 527 MET cc_start: 0.2981 (tpp) cc_final: 0.2668 (tpp) REVERT: E 97 TRP cc_start: 0.8134 (OUTLIER) cc_final: 0.7024 (m-90) REVERT: E 123 GLU cc_start: 0.7442 (mp0) cc_final: 0.7209 (mp0) REVERT: E 139 MET cc_start: 0.6309 (ttm) cc_final: 0.6049 (tpp) REVERT: E 217 MET cc_start: 0.8605 (mtt) cc_final: 0.6603 (ptt) REVERT: E 272 ASP cc_start: 0.8478 (m-30) cc_final: 0.8205 (m-30) REVERT: G 97 TRP cc_start: 0.7963 (OUTLIER) cc_final: 0.7107 (m-90) REVERT: G 139 MET cc_start: 0.6591 (ttm) cc_final: 0.6135 (tpp) REVERT: G 217 MET cc_start: 0.8537 (mtt) cc_final: 0.6665 (tmm) REVERT: B 71 MET cc_start: 0.1339 (ttp) cc_final: 0.1008 (ttp) outliers start: 60 outliers final: 34 residues processed: 225 average time/residue: 0.2733 time to fit residues: 94.5289 Evaluate side-chains 206 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain C residue 97 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 334 HIS Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 97 TRP Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 CYS Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain B residue 116 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 5.9990 chunk 134 optimal weight: 0.2980 chunk 92 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4807 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16744 Z= 0.162 Angle : 0.533 12.539 22596 Z= 0.264 Chirality : 0.035 0.173 2488 Planarity : 0.003 0.034 2832 Dihedral : 12.249 127.246 2346 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.17 % Favored : 98.63 % Rotamer: Outliers : 2.65 % Allowed : 22.23 % Favored : 75.12 % 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: 2.89 (0.19), residues: 1968 helix: 2.12 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : 1.50 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 350 HIS 0.012 0.001 HIS E 334 PHE 0.012 0.001 PHE G 137 TYR 0.015 0.001 TYR C 80 ARG 0.003 0.000 ARG E 331 *********************** 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 232 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 187 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 TRP cc_start: 0.8081 (OUTLIER) cc_final: 0.7302 (m-90) REVERT: A 217 MET cc_start: 0.8465 (mtt) cc_final: 0.6380 (tmm) REVERT: C 217 MET cc_start: 0.8574 (mtt) cc_final: 0.6357 (tmm) REVERT: C 527 MET cc_start: 0.2195 (tpp) cc_final: 0.1923 (ttp) REVERT: E 97 TRP cc_start: 0.8135 (OUTLIER) cc_final: 0.7052 (m-90) REVERT: E 123 GLU cc_start: 0.7515 (mp0) cc_final: 0.7270 (mp0) REVERT: E 217 MET cc_start: 0.8670 (mtt) cc_final: 0.6663 (ptt) REVERT: E 272 ASP cc_start: 0.8524 (m-30) cc_final: 0.8270 (m-30) REVERT: G 97 TRP cc_start: 0.8000 (OUTLIER) cc_final: 0.7314 (m-90) REVERT: G 139 MET cc_start: 0.6561 (ttm) cc_final: 0.6080 (tpp) REVERT: G 217 MET cc_start: 0.8608 (mtt) cc_final: 0.6622 (tmm) REVERT: H 71 MET cc_start: 0.1085 (ttt) cc_final: 0.0831 (ttt) outliers start: 45 outliers final: 25 residues processed: 216 average time/residue: 0.2689 time to fit residues: 88.8399 Evaluate side-chains 202 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 97 TRP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 97 TRP Chi-restraints excluded: chain G residue 156 CYS Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 170 optimal weight: 0.0670 chunk 47 optimal weight: 0.0970 overall best weight: 0.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4810 moved from start: 0.4333 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= 0.155 Angle : 0.528 12.120 22596 Z= 0.262 Chirality : 0.035 0.157 2488 Planarity : 0.003 0.025 2832 Dihedral : 11.497 119.807 2340 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.07 % Favored : 98.73 % Rotamer: Outliers : 3.01 % Allowed : 21.70 % Favored : 75.29 % 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: 2.86 (0.19), residues: 1968 helix: 2.18 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : 1.17 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 350 HIS 0.005 0.001 HIS E 334 PHE 0.013 0.001 PHE G 137 TYR 0.014 0.001 TYR G 80 ARG 0.004 0.000 ARG C 213 *********************** 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 233 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 182 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.6809 (tpp) cc_final: 0.6293 (mmt) REVERT: A 217 MET cc_start: 0.8669 (mtt) cc_final: 0.6725 (tmm) REVERT: C 97 TRP cc_start: 0.7827 (t-100) cc_final: 0.7411 (m100) REVERT: C 137 PHE cc_start: 0.6196 (t80) cc_final: 0.5974 (t80) REVERT: C 217 MET cc_start: 0.8567 (mtt) cc_final: 0.6337 (tmm) REVERT: E 123 GLU cc_start: 0.7570 (mp0) cc_final: 0.7267 (mp0) REVERT: E 217 MET cc_start: 0.8722 (mtt) cc_final: 0.6675 (ptt) REVERT: E 272 ASP cc_start: 0.8502 (m-30) cc_final: 0.8239 (m-30) REVERT: G 139 MET cc_start: 0.6545 (ttm) cc_final: 0.6017 (tpp) REVERT: G 217 MET cc_start: 0.8768 (mtt) cc_final: 0.6788 (tmm) REVERT: D 71 MET cc_start: 0.1399 (tmm) cc_final: 0.0876 (tmm) REVERT: F 71 MET cc_start: 0.1121 (ttt) cc_final: 0.0883 (ttt) REVERT: H 76 MET cc_start: 0.2782 (mpp) cc_final: 0.0764 (mmt) REVERT: H 145 MET cc_start: 0.1531 (OUTLIER) cc_final: -0.0001 (tmm) outliers start: 51 outliers final: 39 residues processed: 225 average time/residue: 0.2335 time to fit residues: 84.3999 Evaluate side-chains 213 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 CYS Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 189 optimal weight: 0.3980 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 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: 0.4893 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16744 Z= 0.260 Angle : 0.577 11.715 22596 Z= 0.286 Chirality : 0.036 0.175 2488 Planarity : 0.003 0.029 2832 Dihedral : 11.117 121.657 2332 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 4.36 % Allowed : 21.64 % Favored : 74.00 % 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: 2.64 (0.19), residues: 1968 helix: 2.07 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : 0.92 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 163 HIS 0.005 0.001 HIS E 334 PHE 0.031 0.002 PHE E 143 TYR 0.020 0.001 TYR C 80 ARG 0.003 0.000 ARG H 74 *********************** 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 244 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 170 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.8757 (mtt) cc_final: 0.6850 (ptt) REVERT: C 97 TRP cc_start: 0.7961 (OUTLIER) cc_final: 0.7440 (m100) REVERT: C 137 PHE cc_start: 0.6368 (t80) cc_final: 0.6135 (t80) REVERT: C 217 MET cc_start: 0.8617 (mtt) cc_final: 0.6453 (ptt) REVERT: E 123 GLU cc_start: 0.7600 (mp0) cc_final: 0.7353 (mp0) REVERT: E 217 MET cc_start: 0.8742 (mtt) cc_final: 0.6707 (ptt) REVERT: G 139 MET cc_start: 0.6459 (ttm) cc_final: 0.6042 (tpp) REVERT: G 217 MET cc_start: 0.8784 (mtt) cc_final: 0.6857 (ptt) REVERT: B 71 MET cc_start: 0.1508 (ttp) cc_final: 0.1126 (ttp) REVERT: D 71 MET cc_start: 0.2400 (tmm) cc_final: 0.1565 (tmm) REVERT: H 76 MET cc_start: 0.2557 (mpp) cc_final: 0.0966 (mmt) REVERT: H 145 MET cc_start: 0.1721 (OUTLIER) cc_final: 0.0111 (tmm) outliers start: 74 outliers final: 62 residues processed: 233 average time/residue: 0.2538 time to fit residues: 91.7944 Evaluate side-chains 222 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 158 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 160 TYR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 112 CYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 156 CYS Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 208 PHE Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 0.3980 chunk 138 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 0.4980 chunk 105 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 118 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4855 moved from start: 0.4864 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= 0.165 Angle : 0.541 12.036 22596 Z= 0.265 Chirality : 0.034 0.166 2488 Planarity : 0.003 0.032 2832 Dihedral : 10.745 116.611 2332 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.27 % Favored : 98.58 % Rotamer: Outliers : 3.77 % Allowed : 22.29 % Favored : 73.94 % 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: 2.82 (0.19), residues: 1968 helix: 2.17 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : 1.10 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 350 HIS 0.003 0.001 HIS E 334 PHE 0.019 0.001 PHE G 137 TYR 0.013 0.001 TYR C 80 ARG 0.009 0.000 ARG C 213 *********************** 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 238 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 174 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.6938 (tpp) cc_final: 0.6453 (mmt) REVERT: A 217 MET cc_start: 0.8782 (mtt) cc_final: 0.6867 (ptt) REVERT: C 97 TRP cc_start: 0.7914 (OUTLIER) cc_final: 0.7370 (m100) REVERT: C 137 PHE cc_start: 0.6318 (t80) cc_final: 0.6094 (t80) REVERT: C 217 MET cc_start: 0.8677 (mtt) cc_final: 0.6543 (ptt) REVERT: E 123 GLU cc_start: 0.7531 (mp0) cc_final: 0.7309 (mp0) REVERT: E 217 MET cc_start: 0.8765 (mtt) cc_final: 0.6711 (ptt) REVERT: E 272 ASP cc_start: 0.8577 (m-30) cc_final: 0.8320 (m-30) REVERT: G 139 MET cc_start: 0.6562 (ttm) cc_final: 0.5980 (tpp) REVERT: G 217 MET cc_start: 0.8841 (mtt) cc_final: 0.6881 (ptt) REVERT: B 71 MET cc_start: 0.1407 (ttp) cc_final: 0.1049 (ttp) REVERT: B 76 MET cc_start: 0.2501 (mpp) cc_final: 0.0702 (mmt) REVERT: F 76 MET cc_start: 0.2730 (mpp) cc_final: 0.0778 (mmt) REVERT: H 76 MET cc_start: 0.2067 (mpp) cc_final: 0.1041 (mmt) REVERT: H 145 MET cc_start: 0.1711 (OUTLIER) cc_final: 0.0203 (tmm) outliers start: 64 outliers final: 51 residues processed: 225 average time/residue: 0.2479 time to fit residues: 87.6330 Evaluate side-chains 221 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 168 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 156 CYS Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 160 TYR Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 156 CYS Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 208 PHE Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** C 569 HIS ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4866 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16744 Z= 0.182 Angle : 0.551 11.983 22596 Z= 0.268 Chirality : 0.035 0.180 2488 Planarity : 0.003 0.026 2832 Dihedral : 10.311 114.156 2332 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.47 % Favored : 98.37 % Rotamer: Outliers : 4.19 % Allowed : 22.35 % Favored : 73.47 % 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: 2.83 (0.19), residues: 1968 helix: 2.18 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : 1.07 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 350 HIS 0.004 0.001 HIS B 107 PHE 0.018 0.001 PHE G 137 TYR 0.014 0.001 TYR C 80 ARG 0.006 0.000 ARG C 213 *********************** 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 239 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 168 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.6929 (tpp) cc_final: 0.6379 (mmt) REVERT: A 217 MET cc_start: 0.8781 (mtt) cc_final: 0.6888 (ptt) REVERT: A 527 MET cc_start: 0.2448 (ttp) cc_final: 0.1827 (tmm) REVERT: C 97 TRP cc_start: 0.8034 (OUTLIER) cc_final: 0.7424 (m100) REVERT: C 137 PHE cc_start: 0.6344 (t80) cc_final: 0.6120 (t80) REVERT: C 217 MET cc_start: 0.8630 (mtt) cc_final: 0.6493 (ptt) REVERT: E 123 GLU cc_start: 0.7593 (mp0) cc_final: 0.7363 (mp0) REVERT: E 217 MET cc_start: 0.8838 (mtt) cc_final: 0.6907 (ptt) REVERT: E 272 ASP cc_start: 0.8624 (m-30) cc_final: 0.8367 (m-30) REVERT: G 139 MET cc_start: 0.6557 (ttm) cc_final: 0.5990 (tpp) REVERT: G 217 MET cc_start: 0.8835 (mtt) cc_final: 0.6800 (ptt) REVERT: D 76 MET cc_start: 0.2775 (mpp) cc_final: 0.1512 (mmp) REVERT: F 76 MET cc_start: 0.2474 (mpp) cc_final: 0.0797 (mmt) REVERT: H 76 MET cc_start: 0.2210 (mpp) cc_final: 0.1304 (mmt) REVERT: H 145 MET cc_start: 0.1582 (OUTLIER) cc_final: 0.0168 (tmm) outliers start: 71 outliers final: 66 residues processed: 230 average time/residue: 0.2504 time to fit residues: 90.7108 Evaluate side-chains 227 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 159 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 TRP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 160 TYR Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 156 CYS Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 208 PHE Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 chunk 54 optimal weight: 0.4980 chunk 159 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 HIS G 334 HIS ** 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: 0.4959 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16744 Z= 0.364 Angle : 0.651 11.559 22596 Z= 0.324 Chirality : 0.038 0.194 2488 Planarity : 0.004 0.033 2832 Dihedral : 10.432 120.516 2332 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.78 % Favored : 98.07 % Rotamer: Outliers : 4.54 % Allowed : 22.41 % Favored : 73.05 % 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: 2.21 (0.19), residues: 1968 helix: 1.71 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : 0.93 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 350 HIS 0.009 0.001 HIS F 107 PHE 0.027 0.002 PHE E 143 TYR 0.026 0.002 TYR C 80 ARG 0.008 0.001 ARG C 213 *********************** 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 227 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 150 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.8786 (mtt) cc_final: 0.6993 (ptt) REVERT: C 97 TRP cc_start: 0.8202 (OUTLIER) cc_final: 0.6849 (m-90) REVERT: C 217 MET cc_start: 0.8663 (mtt) cc_final: 0.6611 (ptt) REVERT: E 139 MET cc_start: 0.6917 (tpp) cc_final: 0.6414 (mmt) REVERT: E 217 MET cc_start: 0.8830 (mtt) cc_final: 0.6892 (ptt) REVERT: G 217 MET cc_start: 0.8875 (mtt) cc_final: 0.7030 (ptt) REVERT: B 71 MET cc_start: 0.2034 (ttp) cc_final: 0.1659 (ttp) REVERT: D 76 MET cc_start: 0.2892 (mpp) cc_final: 0.1465 (mmp) REVERT: F 76 MET cc_start: 0.2575 (mpp) cc_final: 0.0625 (mmt) REVERT: H 145 MET cc_start: 0.1633 (OUTLIER) cc_final: -0.0268 (tmm) outliers start: 77 outliers final: 68 residues processed: 217 average time/residue: 0.2369 time to fit residues: 82.8946 Evaluate side-chains 215 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 145 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 TRP Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 334 HIS Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 112 CYS Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 156 CYS Chi-restraints excluded: chain E residue 160 TYR Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 112 CYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 156 CYS Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 208 PHE Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 334 HIS Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4892 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16744 Z= 0.186 Angle : 0.563 12.071 22596 Z= 0.275 Chirality : 0.035 0.142 2488 Planarity : 0.003 0.029 2832 Dihedral : 10.144 117.386 2332 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.12 % Favored : 98.73 % Rotamer: Outliers : 3.12 % Allowed : 24.00 % Favored : 72.88 % 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: 2.55 (0.19), residues: 1968 helix: 1.92 (0.13), residues: 1488 sheet: None (None), residues: 0 loop : 1.19 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 350 HIS 0.008 0.001 HIS C 334 PHE 0.020 0.001 PHE E 143 TYR 0.014 0.001 TYR C 80 ARG 0.006 0.000 ARG C 213 ********************** 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 213 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 160 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.6979 (tpp) cc_final: 0.6436 (mmt) REVERT: A 217 MET cc_start: 0.8807 (mtt) cc_final: 0.6996 (ptt) REVERT: A 554 ARG cc_start: 0.3339 (OUTLIER) cc_final: 0.2830 (ptm-80) REVERT: C 97 TRP cc_start: 0.8118 (OUTLIER) cc_final: 0.6898 (m-90) REVERT: C 217 MET cc_start: 0.8657 (mtt) cc_final: 0.6531 (ptt) REVERT: E 217 MET cc_start: 0.8874 (mtt) cc_final: 0.7004 (ptt) REVERT: E 272 ASP cc_start: 0.8625 (m-30) cc_final: 0.8373 (m-30) REVERT: G 217 MET cc_start: 0.8885 (mtt) cc_final: 0.6962 (ptt) REVERT: B 51 MET cc_start: 0.2512 (ppp) cc_final: 0.2179 (ppp) REVERT: B 71 MET cc_start: 0.1870 (ttp) cc_final: 0.1515 (ttp) REVERT: B 76 MET cc_start: 0.2097 (mmt) cc_final: 0.1281 (mmt) REVERT: D 76 MET cc_start: 0.2934 (mpp) cc_final: 0.1358 (mmp) REVERT: F 76 MET cc_start: 0.2503 (mpp) cc_final: 0.0485 (mmt) REVERT: H 145 MET cc_start: 0.1680 (OUTLIER) cc_final: -0.0113 (tmm) outliers start: 53 outliers final: 46 residues processed: 205 average time/residue: 0.2327 time to fit residues: 77.2132 Evaluate side-chains 206 residues out of total 1696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 157 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 TRP Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 160 TYR Chi-restraints excluded: chain E residue 208 PHE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 208 PHE Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 334 HIS Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain H residue 145 MET 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: 3.9990 chunk 47 optimal weight: 0.0040 chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 HIS ** G 564 GLN ** 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 = 0.4665 r_free = 0.4665 target = 0.223817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122568 restraints weight = 23297.158| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.65 r_work: 0.3264 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 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 = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16744 Z= 0.165 Angle : 0.545 12.018 22596 Z= 0.264 Chirality : 0.034 0.160 2488 Planarity : 0.003 0.026 2832 Dihedral : 9.767 113.989 2332 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.37 % Favored : 98.48 % Rotamer: Outliers : 2.83 % Allowed : 24.35 % Favored : 72.82 % 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: 2.06 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : 1.19 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 350 HIS 0.006 0.001 HIS F 107 PHE 0.018 0.001 PHE A 137 TYR 0.013 0.001 TYR C 80 ARG 0.005 0.000 ARG A 554 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3837.25 seconds wall clock time: 70 minutes 6.91 seconds (4206.91 seconds total)