Starting phenix.real_space_refine on Wed Mar 20 10:24:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npf_12515/03_2024/7npf_12515_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npf_12515/03_2024/7npf_12515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npf_12515/03_2024/7npf_12515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npf_12515/03_2024/7npf_12515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npf_12515/03_2024/7npf_12515_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7npf_12515/03_2024/7npf_12515_neut_updated.pdb" } resolution = 4.5 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 ------------------------------------------------------------------------------- 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= 1.000 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: 6 Type Number sf(0) Gaussians P 122 5.49 5 Mg 8 5.21 5 S 168 5.16 5 C 16504 2.51 5 N 4551 2.21 5 O 5420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26773 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3070 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3118 Chain: "B" Number of atoms: 3057 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3105 Chain: "C" Number of atoms: 3070 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3118 Chain: "D" Number of atoms: 3057 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3105 Chain: "E" Number of atoms: 3070 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3118 Chain: "F" Number of atoms: 3057 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3105 Chain: "G" Number of atoms: 3070 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 404, 3065 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 386} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3118 Chain: "H" Number of atoms: 3057 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 402, 3052 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 3105 Chain: "I" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1029 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "J" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 980 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AALA A 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 272 " occ=0.50 residue: pdb=" N AALA B 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA B 272 " occ=0.50 residue: pdb=" N AALA C 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA C 272 " occ=0.50 residue: pdb=" N AALA D 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D 272 " occ=0.50 residue: pdb=" N AALA E 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA E 272 " occ=0.50 residue: pdb=" N AALA F 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA F 272 " occ=0.50 residue: pdb=" N AALA G 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA G 272 " occ=0.50 residue: pdb=" N AALA H 272 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA H 272 " occ=0.50 Time building chain proxies: 24.58, per 1000 atoms: 0.92 Number of scatterers: 26773 At special positions: 0 Unit cell: (145.6, 141.44, 206.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 168 16.00 P 122 15.00 Mg 8 11.99 O 5420 8.00 N 4551 7.00 C 16504 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.71 Conformation dependent library (CDL) restraints added in 8.9 seconds 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 16 sheets defined 48.5% alpha, 4.7% beta 26 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 11.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 4.719A pdb=" N GLN A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 55 through 67 Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 124 through 137 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 214 through 229 Processing helix chain 'A' and resid 234 through 247 removed outlier: 3.733A pdb=" N LEU A 239 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 241 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 243 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE A 244 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP A 245 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 284 through 303 Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 326 through 338 Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 376 through 399 Processing helix chain 'A' and resid 403 through 406 No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.702A pdb=" N GLN B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.595A pdb=" N LEU B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 191 through 197 Processing helix chain 'B' and resid 214 through 229 Processing helix chain 'B' and resid 234 through 250 removed outlier: 3.630A pdb=" N LEU B 239 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 241 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 242 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE B 244 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP B 245 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA B 248 " --> pdb=" O ASP B 245 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER B 249 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 250 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 284 through 302 Proline residue: B 298 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 377 through 406 removed outlier: 4.862A pdb=" N SER B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 33 removed outlier: 4.719A pdb=" N GLN C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 55 through 67 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 124 through 137 Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 191 through 197 Processing helix chain 'C' and resid 214 through 229 Processing helix chain 'C' and resid 234 through 247 removed outlier: 3.734A pdb=" N LEU C 239 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU C 241 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 243 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE C 244 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP C 245 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 284 through 303 Proline residue: C 298 - end of helix Processing helix chain 'C' and resid 326 through 338 Processing helix chain 'C' and resid 352 through 359 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 376 through 399 Processing helix chain 'C' and resid 403 through 406 No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'D' and resid 6 through 33 removed outlier: 3.703A pdb=" N GLN D 21 " --> pdb=" O GLN D 17 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 22 " --> pdb=" O LEU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 50 Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'D' and resid 84 through 93 Processing helix chain 'D' and resid 124 through 137 removed outlier: 3.595A pdb=" N LEU D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 191 through 197 Processing helix chain 'D' and resid 214 through 229 Processing helix chain 'D' and resid 234 through 250 removed outlier: 3.630A pdb=" N LEU D 239 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 241 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 242 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE D 244 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP D 245 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 248 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER D 249 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 250 " --> pdb=" O ILE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 284 through 302 Proline residue: D 298 - end of helix Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 352 through 359 Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 377 through 406 removed outlier: 4.861A pdb=" N SER D 403 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 406 " --> pdb=" O SER D 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 33 removed outlier: 4.719A pdb=" N GLN E 21 " --> pdb=" O GLN E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 Processing helix chain 'E' and resid 55 through 67 Processing helix chain 'E' and resid 84 through 94 Processing helix chain 'E' and resid 124 through 137 Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 191 through 197 Processing helix chain 'E' and resid 214 through 229 Processing helix chain 'E' and resid 234 through 247 removed outlier: 3.734A pdb=" N LEU E 239 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 241 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU E 243 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE E 244 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP E 245 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 272 Processing helix chain 'E' and resid 284 through 303 Proline residue: E 298 - end of helix Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 352 through 359 Processing helix chain 'E' and resid 364 through 366 No H-bonds generated for 'chain 'E' and resid 364 through 366' Processing helix chain 'E' and resid 376 through 399 Processing helix chain 'E' and resid 403 through 406 No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'F' and resid 6 through 33 removed outlier: 3.704A pdb=" N GLN F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 55 through 65 Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'F' and resid 124 through 137 removed outlier: 3.594A pdb=" N LEU F 137 " --> pdb=" O ALA F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 Processing helix chain 'F' and resid 191 through 197 Processing helix chain 'F' and resid 214 through 229 Processing helix chain 'F' and resid 234 through 250 removed outlier: 3.630A pdb=" N LEU F 239 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 241 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS F 242 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE F 244 " --> pdb=" O GLU F 241 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASP F 245 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA F 248 " --> pdb=" O ASP F 245 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER F 249 " --> pdb=" O LYS F 246 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP F 250 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 272 Processing helix chain 'F' and resid 284 through 302 Proline residue: F 298 - end of helix Processing helix chain 'F' and resid 326 through 338 Processing helix chain 'F' and resid 352 through 359 Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 377 through 406 removed outlier: 4.861A pdb=" N SER F 403 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 33 removed outlier: 4.719A pdb=" N GLN G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 50 Processing helix chain 'G' and resid 55 through 67 Processing helix chain 'G' and resid 84 through 94 Processing helix chain 'G' and resid 124 through 137 Processing helix chain 'G' and resid 175 through 180 Processing helix chain 'G' and resid 191 through 197 Processing helix chain 'G' and resid 214 through 229 Processing helix chain 'G' and resid 234 through 247 removed outlier: 3.734A pdb=" N LEU G 239 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU G 241 " --> pdb=" O LEU G 238 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU G 243 " --> pdb=" O LYS G 240 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE G 244 " --> pdb=" O GLU G 241 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP G 245 " --> pdb=" O LYS G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 272 Processing helix chain 'G' and resid 284 through 303 Proline residue: G 298 - end of helix Processing helix chain 'G' and resid 326 through 338 Processing helix chain 'G' and resid 352 through 359 Processing helix chain 'G' and resid 364 through 366 No H-bonds generated for 'chain 'G' and resid 364 through 366' Processing helix chain 'G' and resid 376 through 399 Processing helix chain 'G' and resid 403 through 406 No H-bonds generated for 'chain 'G' and resid 403 through 406' Processing helix chain 'H' and resid 6 through 33 removed outlier: 3.702A pdb=" N GLN H 21 " --> pdb=" O GLN H 17 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL H 22 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 50 Processing helix chain 'H' and resid 55 through 65 Processing helix chain 'H' and resid 84 through 93 Processing helix chain 'H' and resid 124 through 137 removed outlier: 3.595A pdb=" N LEU H 137 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 180 Processing helix chain 'H' and resid 191 through 197 Processing helix chain 'H' and resid 214 through 229 Processing helix chain 'H' and resid 234 through 250 removed outlier: 3.630A pdb=" N LEU H 239 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU H 241 " --> pdb=" O LEU H 238 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS H 242 " --> pdb=" O LEU H 239 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE H 244 " --> pdb=" O GLU H 241 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASP H 245 " --> pdb=" O LYS H 242 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA H 248 " --> pdb=" O ASP H 245 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER H 249 " --> pdb=" O LYS H 246 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP H 250 " --> pdb=" O ILE H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 272 Processing helix chain 'H' and resid 284 through 302 Proline residue: H 298 - end of helix Processing helix chain 'H' and resid 326 through 338 Processing helix chain 'H' and resid 352 through 359 Processing helix chain 'H' and resid 369 through 371 No H-bonds generated for 'chain 'H' and resid 369 through 371' Processing helix chain 'H' and resid 377 through 406 removed outlier: 4.861A pdb=" N SER H 403 " --> pdb=" O SER H 399 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN H 406 " --> pdb=" O SER H 402 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 145 through 148 Processing sheet with id= B, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.842A pdb=" N ARG A 315 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 111 through 116 removed outlier: 3.582A pdb=" N THR A 258 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.972A pdb=" N LYS B 208 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 147 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 210 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 145 through 148 Processing sheet with id= F, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.841A pdb=" N ARG C 315 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 111 through 116 removed outlier: 3.582A pdb=" N THR C 258 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 275 through 277 removed outlier: 3.971A pdb=" N LYS D 208 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 147 " --> pdb=" O LYS D 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 210 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 145 through 148 Processing sheet with id= J, first strand: chain 'E' and resid 276 through 278 removed outlier: 3.842A pdb=" N ARG E 315 " --> pdb=" O LEU E 276 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 111 through 116 removed outlier: 3.581A pdb=" N THR E 258 " --> pdb=" O VAL E 115 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 275 through 277 removed outlier: 3.972A pdb=" N LYS F 208 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU F 147 " --> pdb=" O LYS F 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 210 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 145 through 148 Processing sheet with id= N, first strand: chain 'G' and resid 276 through 278 removed outlier: 3.842A pdb=" N ARG G 315 " --> pdb=" O LEU G 276 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 111 through 116 removed outlier: 3.582A pdb=" N THR G 258 " --> pdb=" O VAL G 115 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 275 through 277 removed outlier: 3.971A pdb=" N LYS H 208 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU H 147 " --> pdb=" O LYS H 208 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE H 210 " --> pdb=" O LEU H 147 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 2772 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 8.55 Time building geometry restraints manager: 12.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 8927 1.36 - 1.50: 7561 1.50 - 1.65: 10720 1.65 - 1.80: 185 1.80 - 1.95: 111 Bond restraints: 27504 Sorted by residual: bond pdb=" C3' DT J 19 " pdb=" O3' DT J 19 " ideal model delta sigma weight residual 1.422 1.545 -0.123 3.00e-02 1.11e+03 1.68e+01 bond pdb=" C3' DA I 19 " pdb=" O3' DA I 19 " ideal model delta sigma weight residual 1.422 1.525 -0.103 3.00e-02 1.11e+03 1.19e+01 bond pdb=" C3' DA I 48 " pdb=" O3' DA I 48 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.66e+00 bond pdb=" C3' DT J 29 " pdb=" O3' DT J 29 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" C2' DA I 20 " pdb=" C1' DA I 20 " ideal model delta sigma weight residual 1.525 1.492 0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 27499 not shown) Histogram of bond angle deviations from ideal: 95.87 - 103.53: 642 103.53 - 111.20: 11552 111.20 - 118.86: 11089 118.86 - 126.53: 14032 126.53 - 134.19: 672 Bond angle restraints: 37987 Sorted by residual: angle pdb=" OP1 DT J 20 " pdb=" P DT J 20 " pdb=" O5' DT J 20 " ideal model delta sigma weight residual 109.00 95.87 13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" N GLN F 383 " pdb=" CA GLN F 383 " pdb=" CB GLN F 383 " ideal model delta sigma weight residual 110.39 116.99 -6.60 1.66e+00 3.63e-01 1.58e+01 angle pdb=" N GLN D 383 " pdb=" CA GLN D 383 " pdb=" CB GLN D 383 " ideal model delta sigma weight residual 110.39 116.98 -6.59 1.66e+00 3.63e-01 1.57e+01 angle pdb=" N GLN H 383 " pdb=" CA GLN H 383 " pdb=" CB GLN H 383 " ideal model delta sigma weight residual 110.39 116.96 -6.57 1.66e+00 3.63e-01 1.57e+01 angle pdb=" N GLN B 383 " pdb=" CA GLN B 383 " pdb=" CB GLN B 383 " ideal model delta sigma weight residual 110.39 116.94 -6.55 1.66e+00 3.63e-01 1.56e+01 ... (remaining 37982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.30: 15531 33.30 - 66.60: 828 66.60 - 99.90: 52 99.90 - 133.21: 1 133.21 - 166.51: 10 Dihedral angle restraints: 16422 sinusoidal: 6878 harmonic: 9544 Sorted by residual: dihedral pdb=" CA THR E 8 " pdb=" C THR E 8 " pdb=" N ILE E 9 " pdb=" CA ILE E 9 " ideal model delta harmonic sigma weight residual 180.00 141.40 38.60 0 5.00e+00 4.00e-02 5.96e+01 dihedral pdb=" CA THR C 8 " pdb=" C THR C 8 " pdb=" N ILE C 9 " pdb=" CA ILE C 9 " ideal model delta harmonic sigma weight residual 180.00 141.41 38.59 0 5.00e+00 4.00e-02 5.96e+01 dihedral pdb=" CA THR G 8 " pdb=" C THR G 8 " pdb=" N ILE G 9 " pdb=" CA ILE G 9 " ideal model delta harmonic sigma weight residual 180.00 141.44 38.56 0 5.00e+00 4.00e-02 5.95e+01 ... (remaining 16419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3663 0.065 - 0.130: 651 0.130 - 0.195: 95 0.195 - 0.260: 9 0.260 - 0.325: 10 Chirality restraints: 4428 Sorted by residual: chirality pdb=" C1' DA I 32 " pdb=" O4' DA I 32 " pdb=" C2' DA I 32 " pdb=" N9 DA I 32 " both_signs ideal model delta sigma weight residual False 2.42 2.09 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C1' DT J 31 " pdb=" O4' DT J 31 " pdb=" C2' DT J 31 " pdb=" N1 DT J 31 " both_signs ideal model delta sigma weight residual False 2.47 2.14 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" P DA I 49 " pdb=" OP1 DA I 49 " pdb=" OP2 DA I 49 " pdb=" O5' DA I 49 " both_signs ideal model delta sigma weight residual True 2.35 -2.65 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 4425 not shown) Planarity restraints: 4598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 5 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ARG A 5 " 0.066 2.00e-02 2.50e+03 pdb=" O ARG A 5 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU A 6 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 5 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ARG C 5 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG C 5 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU C 6 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 5 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C ARG E 5 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG E 5 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU E 6 " 0.021 2.00e-02 2.50e+03 ... (remaining 4595 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 487 2.58 - 3.16: 25494 3.16 - 3.74: 44821 3.74 - 4.32: 60642 4.32 - 4.90: 93004 Nonbonded interactions: 224448 Sorted by model distance: nonbonded pdb=" O VAL D 115 " pdb="MG MG D 501 " model vdw 1.998 2.170 nonbonded pdb=" O VAL F 115 " pdb="MG MG F 501 " model vdw 1.998 2.170 nonbonded pdb=" O VAL B 115 " pdb="MG MG B 501 " model vdw 1.999 2.170 nonbonded pdb=" O VAL H 115 " pdb="MG MG H 501 " model vdw 1.999 2.170 nonbonded pdb="MG MG A 501 " pdb=" O1B AGS A 502 " model vdw 2.021 2.170 ... (remaining 224443 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 4 through 271 or resid 273 through 372 or resid 375 throug \ h 407 or resid 501 through 502)) selection = (chain 'B' and (resid 4 through 271 or resid 273 through 407 or resid 501 throug \ h 502)) selection = (chain 'C' and (resid 4 through 271 or resid 273 through 372 or resid 375 throug \ h 407 or resid 501 through 502)) selection = (chain 'D' and (resid 4 through 271 or resid 273 through 407 or resid 501 throug \ h 502)) selection = (chain 'E' and (resid 4 through 271 or resid 273 through 372 or resid 375 throug \ h 407 or resid 501 through 502)) selection = (chain 'F' and (resid 4 through 271 or resid 273 through 407 or resid 501 throug \ h 502)) selection = (chain 'G' and (resid 4 through 271 or resid 273 through 372 or resid 375 throug \ h 407 or resid 501 through 502)) selection = (chain 'H' and (resid 4 through 271 or resid 273 through 407 or resid 501 throug \ h 502)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 2.610 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 92.860 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.230 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 27504 Z= 0.270 Angle : 0.917 13.131 37987 Z= 0.505 Chirality : 0.053 0.325 4428 Planarity : 0.007 0.067 4598 Dihedral : 19.230 166.507 10174 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.87 % Favored : 91.01 % Rotamer: Outliers : 0.47 % Allowed : 1.66 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.14), residues: 3216 helix: -1.85 (0.12), residues: 1572 sheet: -2.23 (0.29), residues: 268 loop : -1.93 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP C 111 HIS 0.014 0.001 HIS B 398 PHE 0.030 0.003 PHE G 304 TYR 0.010 0.001 TYR B 361 ARG 0.020 0.002 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1036 time to evaluate : 2.967 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8834 (t) cc_final: 0.8369 (p) REVERT: A 27 ILE cc_start: 0.7650 (mt) cc_final: 0.7416 (mt) REVERT: A 78 ASN cc_start: 0.8224 (m-40) cc_final: 0.7506 (t0) REVERT: A 206 ASN cc_start: 0.6923 (p0) cc_final: 0.6544 (p0) REVERT: A 226 TYR cc_start: 0.8573 (m-10) cc_final: 0.8143 (m-80) REVERT: A 250 ASP cc_start: 0.8506 (p0) cc_final: 0.8198 (p0) REVERT: A 355 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8467 (mt-10) REVERT: B 10 GLU cc_start: 0.8656 (mp0) cc_final: 0.7756 (pp20) REVERT: B 17 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8331 (mm-40) REVERT: B 99 PHE cc_start: 0.6217 (t80) cc_final: 0.5986 (t80) REVERT: B 130 HIS cc_start: 0.7470 (m170) cc_final: 0.7190 (m90) REVERT: B 153 GLN cc_start: 0.8511 (mp10) cc_final: 0.8286 (mp10) REVERT: B 190 ASP cc_start: 0.7828 (t0) cc_final: 0.7288 (p0) REVERT: B 191 THR cc_start: 0.8521 (p) cc_final: 0.7909 (t) REVERT: B 192 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8310 (mp0) REVERT: B 216 ASP cc_start: 0.6806 (m-30) cc_final: 0.6537 (m-30) REVERT: B 297 LEU cc_start: 0.7384 (mp) cc_final: 0.7076 (tp) REVERT: B 331 VAL cc_start: 0.8826 (t) cc_final: 0.8036 (t) REVERT: B 387 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7305 (tm-30) REVERT: B 391 LEU cc_start: 0.9353 (mp) cc_final: 0.9107 (mp) REVERT: C 25 ASP cc_start: 0.8536 (m-30) cc_final: 0.8320 (t70) REVERT: C 84 LEU cc_start: 0.8981 (tt) cc_final: 0.8716 (tt) REVERT: C 126 MET cc_start: 0.7752 (tmm) cc_final: 0.6784 (tpp) REVERT: C 199 MET cc_start: 0.7367 (mmm) cc_final: 0.6985 (mmm) REVERT: C 216 ASP cc_start: 0.6686 (m-30) cc_final: 0.6243 (m-30) REVERT: C 226 TYR cc_start: 0.8599 (m-10) cc_final: 0.8055 (m-80) REVERT: C 297 LEU cc_start: 0.7348 (mp) cc_final: 0.7057 (mp) REVERT: C 379 LEU cc_start: 0.7660 (tt) cc_final: 0.7452 (tt) REVERT: C 398 HIS cc_start: 0.7965 (m170) cc_final: 0.7027 (m90) REVERT: D 42 MET cc_start: 0.8088 (mtt) cc_final: 0.6373 (mtp) REVERT: D 199 MET cc_start: 0.5002 (pmm) cc_final: 0.4712 (pmm) REVERT: D 225 GLN cc_start: 0.8568 (mm110) cc_final: 0.8365 (mm-40) REVERT: D 332 LEU cc_start: 0.9176 (tp) cc_final: 0.8875 (tp) REVERT: D 344 MET cc_start: 0.5422 (ttp) cc_final: 0.4681 (tpt) REVERT: E 200 LEU cc_start: 0.7143 (mt) cc_final: 0.6620 (tt) REVERT: E 250 ASP cc_start: 0.8336 (p0) cc_final: 0.8066 (p0) REVERT: E 294 PHE cc_start: 0.7182 (m-80) cc_final: 0.6957 (m-80) REVERT: E 398 HIS cc_start: 0.7701 (m170) cc_final: 0.7407 (m90) REVERT: F 20 GLN cc_start: 0.7627 (mt0) cc_final: 0.7335 (mt0) REVERT: F 25 ASP cc_start: 0.8550 (m-30) cc_final: 0.8291 (m-30) REVERT: F 29 ILE cc_start: 0.8862 (mt) cc_final: 0.8611 (mt) REVERT: F 157 ARG cc_start: 0.7404 (mtm110) cc_final: 0.7204 (mtp180) REVERT: F 225 GLN cc_start: 0.8623 (mm110) cc_final: 0.8369 (mm-40) REVERT: F 331 VAL cc_start: 0.9170 (t) cc_final: 0.8167 (t) REVERT: G 199 MET cc_start: 0.5543 (mmm) cc_final: 0.4891 (mmm) REVERT: G 218 MET cc_start: 0.8170 (tmm) cc_final: 0.7968 (tmm) REVERT: G 226 TYR cc_start: 0.8659 (m-10) cc_final: 0.8356 (m-80) REVERT: G 233 LEU cc_start: 0.7782 (mm) cc_final: 0.7480 (mm) REVERT: H 14 GLN cc_start: 0.7606 (tm-30) cc_final: 0.6985 (pp30) REVERT: H 32 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7489 (mm-30) REVERT: H 46 LEU cc_start: 0.9144 (mt) cc_final: 0.8908 (mt) REVERT: H 47 MET cc_start: 0.8434 (mmm) cc_final: 0.7997 (mmm) REVERT: H 73 THR cc_start: 0.7987 (t) cc_final: 0.7394 (t) REVERT: H 86 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7214 (mt-10) REVERT: H 213 PHE cc_start: 0.7068 (m-80) cc_final: 0.6794 (m-80) REVERT: H 344 MET cc_start: 0.4111 (ttp) cc_final: 0.2747 (ttp) outliers start: 12 outliers final: 1 residues processed: 1040 average time/residue: 0.3784 time to fit residues: 621.0549 Evaluate side-chains 845 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 844 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 276 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 257 optimal weight: 0.6980 chunk 99 optimal weight: 30.0000 chunk 156 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 297 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 387 GLN A 398 HIS B 78 ASN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 406 GLN C 20 GLN C 79 HIS C 161 ASN C 398 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN D 405 ASN D 406 GLN E 7 GLN E 71 GLN E 161 ASN E 342 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN G 383 GLN G 400 HIS H 79 HIS ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 ASN H 406 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 27504 Z= 0.257 Angle : 0.809 11.942 37987 Z= 0.422 Chirality : 0.046 0.278 4428 Planarity : 0.006 0.100 4598 Dihedral : 20.328 169.227 4738 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.32 % Allowed : 3.20 % Favored : 96.48 % 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: -2.14 (0.14), residues: 3216 helix: -1.19 (0.12), residues: 1624 sheet: -1.98 (0.26), residues: 264 loop : -1.39 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 287 HIS 0.013 0.002 HIS A 100 PHE 0.037 0.003 PHE E 293 TYR 0.018 0.002 TYR H 337 ARG 0.013 0.001 ARG H 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 933 time to evaluate : 3.130 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: 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: 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: 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: 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 8 THR cc_start: 0.5714 (m) cc_final: 0.5343 (m) REVERT: A 20 GLN cc_start: 0.8582 (mm110) cc_final: 0.8090 (mm-40) REVERT: A 42 MET cc_start: 0.5601 (mtp) cc_final: 0.5379 (mtp) REVERT: A 78 ASN cc_start: 0.8260 (m-40) cc_final: 0.7705 (t0) REVERT: A 86 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 191 THR cc_start: 0.9043 (p) cc_final: 0.8543 (t) REVERT: A 206 ASN cc_start: 0.6961 (p0) cc_final: 0.6630 (p0) REVERT: A 207 LEU cc_start: 0.7883 (tp) cc_final: 0.7581 (tp) REVERT: A 230 ASN cc_start: 0.5403 (p0) cc_final: 0.5011 (p0) REVERT: A 234 ASP cc_start: 0.8651 (m-30) cc_final: 0.8306 (m-30) REVERT: B 5 ARG cc_start: 0.6548 (ttm170) cc_final: 0.5814 (ttm170) REVERT: B 10 GLU cc_start: 0.8599 (mp0) cc_final: 0.7822 (pp20) REVERT: B 17 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8334 (mm-40) REVERT: B 18 LEU cc_start: 0.8207 (pp) cc_final: 0.7559 (pp) REVERT: B 22 VAL cc_start: 0.8149 (t) cc_final: 0.7248 (t) REVERT: B 130 HIS cc_start: 0.7587 (m170) cc_final: 0.7091 (m90) REVERT: B 139 LEU cc_start: 0.8116 (mp) cc_final: 0.7757 (mp) REVERT: B 153 GLN cc_start: 0.8539 (mp10) cc_final: 0.8150 (mp10) REVERT: B 156 LEU cc_start: 0.7893 (mp) cc_final: 0.7625 (mp) REVERT: B 215 GLU cc_start: 0.8927 (mp0) cc_final: 0.8603 (mp0) REVERT: B 293 PHE cc_start: 0.7888 (t80) cc_final: 0.7605 (t80) REVERT: B 297 LEU cc_start: 0.7664 (mp) cc_final: 0.7416 (tp) REVERT: B 314 VAL cc_start: 0.8338 (t) cc_final: 0.8037 (t) REVERT: B 331 VAL cc_start: 0.8835 (t) cc_final: 0.7965 (t) REVERT: B 341 ASP cc_start: 0.7384 (p0) cc_final: 0.5886 (m-30) REVERT: C 124 LYS cc_start: 0.7470 (ptpp) cc_final: 0.6956 (ptpp) REVERT: C 126 MET cc_start: 0.7873 (tmm) cc_final: 0.6980 (tpp) REVERT: C 179 MET cc_start: 0.7355 (mmp) cc_final: 0.6884 (mmp) REVERT: C 226 TYR cc_start: 0.8599 (m-10) cc_final: 0.8157 (m-80) REVERT: C 241 GLU cc_start: 0.8456 (mp0) cc_final: 0.8010 (mp0) REVERT: C 387 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7378 (tm-30) REVERT: C 398 HIS cc_start: 0.7774 (m-70) cc_final: 0.7144 (m-70) REVERT: D 153 GLN cc_start: 0.7489 (mp10) cc_final: 0.7129 (mp10) REVERT: D 255 MET cc_start: 0.5141 (mtt) cc_final: 0.4594 (mtt) REVERT: D 296 HIS cc_start: 0.8178 (t-90) cc_final: 0.7714 (t-90) REVERT: D 297 LEU cc_start: 0.8393 (mp) cc_final: 0.6983 (mp) REVERT: D 344 MET cc_start: 0.5803 (ttp) cc_final: 0.4920 (tpt) REVERT: E 91 MET cc_start: 0.6184 (mmp) cc_final: 0.5943 (mmp) REVERT: E 159 PHE cc_start: 0.7473 (t80) cc_final: 0.7041 (t80) REVERT: E 161 ASN cc_start: 0.7544 (m-40) cc_final: 0.7218 (m-40) REVERT: E 185 ASP cc_start: 0.7799 (m-30) cc_final: 0.7582 (m-30) REVERT: E 192 GLU cc_start: 0.8211 (mp0) cc_final: 0.7902 (mp0) REVERT: E 250 ASP cc_start: 0.8242 (p0) cc_final: 0.7796 (p0) REVERT: E 344 MET cc_start: 0.6815 (tpp) cc_final: 0.6534 (tpp) REVERT: F 25 ASP cc_start: 0.8494 (m-30) cc_final: 0.8239 (m-30) REVERT: F 157 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7400 (mtp180) REVERT: F 195 ARG cc_start: 0.7287 (mtt90) cc_final: 0.6857 (tpp80) REVERT: F 255 MET cc_start: 0.5148 (mtt) cc_final: 0.4943 (mtt) REVERT: F 320 MET cc_start: 0.5913 (mmp) cc_final: 0.4930 (mmp) REVERT: F 387 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8039 (tm-30) REVERT: G 13 TYR cc_start: 0.7937 (t80) cc_final: 0.7693 (t80) REVERT: G 55 ARG cc_start: 0.7391 (mmm-85) cc_final: 0.6742 (mmt90) REVERT: G 64 LYS cc_start: 0.9268 (tmtt) cc_final: 0.9066 (tmtt) REVERT: G 218 MET cc_start: 0.8343 (tmm) cc_final: 0.8128 (tmm) REVERT: G 226 TYR cc_start: 0.8574 (m-10) cc_final: 0.8208 (m-80) REVERT: G 233 LEU cc_start: 0.7624 (mm) cc_final: 0.7396 (mm) REVERT: G 270 MET cc_start: 0.7694 (mmp) cc_final: 0.7348 (mmm) REVERT: G 406 GLN cc_start: 0.6181 (tm-30) cc_final: 0.5563 (tm-30) REVERT: H 17 GLN cc_start: 0.8663 (mm-40) cc_final: 0.7992 (mt0) REVERT: H 32 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7453 (mm-30) REVERT: H 42 MET cc_start: 0.6202 (ttm) cc_final: 0.5359 (ttt) REVERT: H 192 GLU cc_start: 0.8778 (tp30) cc_final: 0.8563 (tp30) REVERT: H 193 PHE cc_start: 0.8614 (t80) cc_final: 0.8370 (t80) REVERT: H 230 ASN cc_start: 0.7108 (p0) cc_final: 0.6868 (p0) REVERT: H 317 MET cc_start: 0.8764 (ttt) cc_final: 0.8562 (ttt) REVERT: H 325 ASN cc_start: 0.7046 (t0) cc_final: 0.6759 (t0) REVERT: H 344 MET cc_start: 0.4614 (ttp) cc_final: 0.3337 (ttp) REVERT: H 387 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7781 (tm-30) REVERT: H 398 HIS cc_start: 0.7800 (m-70) cc_final: 0.7518 (m-70) outliers start: 8 outliers final: 0 residues processed: 939 average time/residue: 0.3531 time to fit residues: 529.6837 Evaluate side-chains 802 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 802 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 165 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 247 optimal weight: 30.0000 chunk 202 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 298 optimal weight: 0.0000 chunk 322 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 295 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN B 78 ASN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN E 342 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN F 406 GLN G 14 GLN G 383 GLN H 14 GLN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 ASN H 406 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27504 Z= 0.260 Angle : 0.773 9.651 37987 Z= 0.404 Chirality : 0.045 0.233 4428 Planarity : 0.006 0.060 4598 Dihedral : 19.844 172.374 4738 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.28 % Allowed : 2.96 % Favored : 96.76 % 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: -1.55 (0.14), residues: 3216 helix: -0.68 (0.12), residues: 1616 sheet: -1.58 (0.26), residues: 260 loop : -1.18 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP C 401 HIS 0.018 0.002 HIS E 398 PHE 0.046 0.002 PHE D 293 TYR 0.023 0.002 TYR H 337 ARG 0.012 0.001 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 921 time to evaluate : 3.011 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.8218 (t) cc_final: 0.7297 (t) REVERT: A 78 ASN cc_start: 0.8358 (m-40) cc_final: 0.7732 (t0) REVERT: A 191 THR cc_start: 0.9099 (p) cc_final: 0.8869 (p) REVERT: A 192 GLU cc_start: 0.9219 (mp0) cc_final: 0.8950 (pm20) REVERT: A 206 ASN cc_start: 0.6980 (p0) cc_final: 0.6736 (p0) REVERT: A 207 LEU cc_start: 0.7900 (tp) cc_final: 0.7637 (tp) REVERT: A 225 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7829 (tm-30) REVERT: A 230 ASN cc_start: 0.4936 (p0) cc_final: 0.4513 (p0) REVERT: A 234 ASP cc_start: 0.8667 (m-30) cc_final: 0.8380 (m-30) REVERT: B 5 ARG cc_start: 0.6847 (ttm170) cc_final: 0.5998 (ttm170) REVERT: B 10 GLU cc_start: 0.8631 (mp0) cc_final: 0.7732 (pp20) REVERT: B 18 LEU cc_start: 0.8244 (pp) cc_final: 0.7485 (pp) REVERT: B 22 VAL cc_start: 0.8210 (t) cc_final: 0.7464 (t) REVERT: B 42 MET cc_start: 0.7727 (mtt) cc_final: 0.7243 (mtt) REVERT: B 47 MET cc_start: 0.8255 (mpp) cc_final: 0.7598 (mmm) REVERT: B 153 GLN cc_start: 0.8596 (mp10) cc_final: 0.8249 (mp10) REVERT: B 156 LEU cc_start: 0.7939 (mp) cc_final: 0.7688 (mp) REVERT: B 190 ASP cc_start: 0.7424 (p0) cc_final: 0.6677 (p0) REVERT: B 192 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8339 (mp0) REVERT: B 215 GLU cc_start: 0.8954 (mp0) cc_final: 0.8612 (mp0) REVERT: B 293 PHE cc_start: 0.8084 (t80) cc_final: 0.7701 (t80) REVERT: B 297 LEU cc_start: 0.7767 (mp) cc_final: 0.7449 (tp) REVERT: B 313 PHE cc_start: 0.6798 (p90) cc_final: 0.6150 (p90) REVERT: B 331 VAL cc_start: 0.8814 (t) cc_final: 0.7964 (t) REVERT: B 332 LEU cc_start: 0.9195 (tp) cc_final: 0.8938 (tp) REVERT: B 341 ASP cc_start: 0.7391 (p0) cc_final: 0.5963 (m-30) REVERT: B 387 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 391 LEU cc_start: 0.9322 (mp) cc_final: 0.8910 (mp) REVERT: C 124 LYS cc_start: 0.7644 (ptpp) cc_final: 0.7203 (ptpp) REVERT: C 126 MET cc_start: 0.8008 (tmm) cc_final: 0.7075 (tpp) REVERT: C 216 ASP cc_start: 0.6780 (m-30) cc_final: 0.6560 (m-30) REVERT: C 226 TYR cc_start: 0.8764 (m-10) cc_final: 0.8364 (m-80) REVERT: C 241 GLU cc_start: 0.8519 (mp0) cc_final: 0.8155 (mp0) REVERT: D 153 GLN cc_start: 0.7533 (mp10) cc_final: 0.7069 (mp10) REVERT: D 192 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7547 (mm-30) REVERT: D 226 TYR cc_start: 0.8675 (t80) cc_final: 0.8243 (t80) REVERT: D 255 MET cc_start: 0.4970 (mtt) cc_final: 0.4412 (mtt) REVERT: D 293 PHE cc_start: 0.7998 (t80) cc_final: 0.7749 (t80) REVERT: D 344 MET cc_start: 0.5987 (ttp) cc_final: 0.5200 (tpt) REVERT: E 89 MET cc_start: 0.6919 (ttt) cc_final: 0.6594 (ptm) REVERT: E 90 LEU cc_start: 0.7506 (mm) cc_final: 0.7273 (mm) REVERT: E 91 MET cc_start: 0.6346 (mmp) cc_final: 0.6112 (mmp) REVERT: E 192 GLU cc_start: 0.8474 (mp0) cc_final: 0.8239 (mp0) REVERT: E 200 LEU cc_start: 0.7845 (mt) cc_final: 0.7613 (tt) REVERT: E 250 ASP cc_start: 0.8202 (p0) cc_final: 0.7694 (p0) REVERT: E 398 HIS cc_start: 0.8062 (m-70) cc_final: 0.7561 (m-70) REVERT: F 25 ASP cc_start: 0.8454 (m-30) cc_final: 0.8238 (m-30) REVERT: F 119 LYS cc_start: 0.8391 (tptm) cc_final: 0.8136 (tptt) REVERT: F 157 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7550 (mtp180) REVERT: F 195 ARG cc_start: 0.7380 (mtt90) cc_final: 0.6963 (tpp80) REVERT: F 255 MET cc_start: 0.5128 (mtt) cc_final: 0.4893 (mtt) REVERT: F 320 MET cc_start: 0.5783 (mmp) cc_final: 0.5458 (mmp) REVERT: F 387 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8097 (tm-30) REVERT: G 13 TYR cc_start: 0.7950 (t80) cc_final: 0.7741 (t80) REVERT: G 39 PHE cc_start: 0.4782 (m-80) cc_final: 0.4568 (m-80) REVERT: G 55 ARG cc_start: 0.7318 (mmm-85) cc_final: 0.6901 (mmt90) REVERT: G 64 LYS cc_start: 0.9297 (tmtt) cc_final: 0.8825 (tmtt) REVERT: G 65 MET cc_start: 0.8412 (mmm) cc_final: 0.7605 (mmm) REVERT: G 89 MET cc_start: 0.5259 (ppp) cc_final: 0.4909 (ppp) REVERT: G 137 LEU cc_start: 0.7552 (tt) cc_final: 0.7336 (mm) REVERT: G 218 MET cc_start: 0.8382 (tmm) cc_final: 0.8163 (tmm) REVERT: G 226 TYR cc_start: 0.8519 (m-10) cc_final: 0.8088 (m-80) REVERT: G 233 LEU cc_start: 0.7662 (mm) cc_final: 0.7346 (mm) REVERT: G 236 VAL cc_start: 0.7181 (m) cc_final: 0.6302 (m) REVERT: G 406 GLN cc_start: 0.6576 (tm-30) cc_final: 0.6249 (tm-30) REVERT: H 14 GLN cc_start: 0.8116 (tm130) cc_final: 0.7564 (tm-30) REVERT: H 17 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8000 (mt0) REVERT: H 32 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7549 (mm-30) REVERT: H 64 LYS cc_start: 0.8817 (pttm) cc_final: 0.8521 (pttm) REVERT: H 193 PHE cc_start: 0.8658 (t80) cc_final: 0.8315 (t80) REVERT: H 317 MET cc_start: 0.8717 (ttt) cc_final: 0.8202 (ttm) REVERT: H 344 MET cc_start: 0.4770 (ttp) cc_final: 0.4292 (ttp) REVERT: H 367 LEU cc_start: 0.7455 (pt) cc_final: 0.7254 (pt) REVERT: H 387 GLN cc_start: 0.8516 (tm-30) cc_final: 0.7949 (tm-30) REVERT: H 398 HIS cc_start: 0.7787 (m-70) cc_final: 0.7451 (m-70) REVERT: H 404 LEU cc_start: 0.8895 (mm) cc_final: 0.8592 (mm) outliers start: 7 outliers final: 1 residues processed: 927 average time/residue: 0.3610 time to fit residues: 537.3596 Evaluate side-chains 803 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 802 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 294 optimal weight: 20.0000 chunk 224 optimal weight: 0.0570 chunk 154 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 200 optimal weight: 20.0000 chunk 299 optimal weight: 0.3980 chunk 317 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN B 23 GLN B 78 ASN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS C 400 HIS ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN G 292 ASN G 383 GLN H 116 GLN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 GLN H 261 HIS ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27504 Z= 0.216 Angle : 0.756 13.267 37987 Z= 0.391 Chirality : 0.044 0.229 4428 Planarity : 0.005 0.089 4598 Dihedral : 19.471 170.857 4738 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.00 % 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: -1.12 (0.14), residues: 3216 helix: -0.31 (0.12), residues: 1568 sheet: -1.20 (0.27), residues: 260 loop : -1.02 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP H 287 HIS 0.020 0.002 HIS E 398 PHE 0.037 0.002 PHE E 159 TYR 0.019 0.002 TYR E 226 ARG 0.006 0.001 ARG E 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 897 time to evaluate : 2.717 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: 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: 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: 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: 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 22 VAL cc_start: 0.8662 (t) cc_final: 0.7509 (t) REVERT: A 78 ASN cc_start: 0.8390 (m-40) cc_final: 0.7744 (t0) REVERT: A 86 GLU cc_start: 0.7746 (tp30) cc_final: 0.7372 (mm-30) REVERT: A 206 ASN cc_start: 0.6845 (p0) cc_final: 0.6523 (p0) REVERT: A 207 LEU cc_start: 0.7981 (tp) cc_final: 0.7699 (tp) REVERT: A 225 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7841 (tm-30) REVERT: A 230 ASN cc_start: 0.4704 (p0) cc_final: 0.4330 (p0) REVERT: A 234 ASP cc_start: 0.8603 (m-30) cc_final: 0.8278 (m-30) REVERT: A 315 ARG cc_start: 0.5522 (mpt180) cc_final: 0.5250 (mtp85) REVERT: A 394 GLU cc_start: 0.7133 (pp20) cc_final: 0.6906 (pp20) REVERT: B 5 ARG cc_start: 0.6744 (ttm170) cc_final: 0.5889 (ttm170) REVERT: B 10 GLU cc_start: 0.8740 (mp0) cc_final: 0.7727 (pp20) REVERT: B 18 LEU cc_start: 0.8018 (pp) cc_final: 0.7172 (pp) REVERT: B 42 MET cc_start: 0.7558 (mtt) cc_final: 0.6634 (mtt) REVERT: B 99 PHE cc_start: 0.6745 (t80) cc_final: 0.6079 (t80) REVERT: B 153 GLN cc_start: 0.8619 (mp10) cc_final: 0.8263 (mp10) REVERT: B 156 LEU cc_start: 0.7888 (mp) cc_final: 0.7523 (mp) REVERT: B 192 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8366 (mp0) REVERT: B 215 GLU cc_start: 0.8870 (mp0) cc_final: 0.8386 (mp0) REVERT: B 293 PHE cc_start: 0.8102 (t80) cc_final: 0.7621 (t80) REVERT: B 313 PHE cc_start: 0.6629 (p90) cc_final: 0.5970 (p90) REVERT: B 331 VAL cc_start: 0.8737 (t) cc_final: 0.7897 (t) REVERT: B 341 ASP cc_start: 0.7355 (p0) cc_final: 0.5997 (m-30) REVERT: B 387 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7523 (tm-30) REVERT: B 391 LEU cc_start: 0.9300 (mp) cc_final: 0.8836 (mp) REVERT: C 31 LEU cc_start: 0.8357 (mm) cc_final: 0.8140 (mm) REVERT: C 124 LYS cc_start: 0.7403 (ptpp) cc_final: 0.6943 (ptpp) REVERT: C 126 MET cc_start: 0.8000 (tmm) cc_final: 0.6990 (tpp) REVERT: C 179 MET cc_start: 0.7277 (mmp) cc_final: 0.6668 (mmp) REVERT: C 226 TYR cc_start: 0.8738 (m-10) cc_final: 0.8326 (m-80) REVERT: C 241 GLU cc_start: 0.8540 (mp0) cc_final: 0.8136 (mp0) REVERT: C 335 MET cc_start: 0.8221 (mtm) cc_final: 0.7984 (mtm) REVERT: D 153 GLN cc_start: 0.7447 (mp10) cc_final: 0.6838 (mp10) REVERT: D 226 TYR cc_start: 0.8730 (t80) cc_final: 0.8455 (t80) REVERT: D 344 MET cc_start: 0.5908 (ttp) cc_final: 0.5183 (tpt) REVERT: E 89 MET cc_start: 0.6843 (ttt) cc_final: 0.6562 (ppp) REVERT: E 90 LEU cc_start: 0.7406 (mm) cc_final: 0.7114 (mm) REVERT: E 192 GLU cc_start: 0.8404 (mp0) cc_final: 0.8190 (mp0) REVERT: E 250 ASP cc_start: 0.8090 (p0) cc_final: 0.7680 (p0) REVERT: E 398 HIS cc_start: 0.7974 (m-70) cc_final: 0.7520 (m-70) REVERT: F 157 ARG cc_start: 0.7822 (mtm110) cc_final: 0.7551 (mtp180) REVERT: F 195 ARG cc_start: 0.7416 (mtt90) cc_final: 0.6991 (tpp80) REVERT: F 255 MET cc_start: 0.5174 (mtt) cc_final: 0.4895 (mtt) REVERT: F 270 MET cc_start: 0.6105 (ttt) cc_final: 0.5435 (ttt) REVERT: F 320 MET cc_start: 0.5834 (mmp) cc_final: 0.5436 (mmp) REVERT: F 383 GLN cc_start: 0.8908 (pm20) cc_final: 0.8536 (pm20) REVERT: F 387 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8018 (tm-30) REVERT: G 39 PHE cc_start: 0.4602 (m-80) cc_final: 0.4337 (m-80) REVERT: G 55 ARG cc_start: 0.7247 (mmm-85) cc_final: 0.6908 (mmt90) REVERT: G 137 LEU cc_start: 0.7533 (tt) cc_final: 0.7307 (mm) REVERT: G 141 LYS cc_start: 0.3230 (mmmt) cc_final: 0.2799 (mmmt) REVERT: G 218 MET cc_start: 0.8412 (tmm) cc_final: 0.8155 (tmm) REVERT: G 226 TYR cc_start: 0.8494 (m-10) cc_final: 0.8039 (m-80) REVERT: G 234 ASP cc_start: 0.8142 (m-30) cc_final: 0.7864 (m-30) REVERT: H 14 GLN cc_start: 0.7508 (pp30) cc_final: 0.6869 (pp30) REVERT: H 17 GLN cc_start: 0.8700 (mm-40) cc_final: 0.7870 (mm-40) REVERT: H 20 GLN cc_start: 0.7578 (mt0) cc_final: 0.7177 (tm-30) REVERT: H 21 GLN cc_start: 0.9076 (mp-120) cc_final: 0.8610 (mp-120) REVERT: H 28 GLU cc_start: 0.8815 (tm-30) cc_final: 0.7792 (tm-30) REVERT: H 29 ILE cc_start: 0.9038 (mt) cc_final: 0.8742 (mt) REVERT: H 32 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7406 (mm-30) REVERT: H 50 ARG cc_start: 0.7828 (ptp-110) cc_final: 0.7434 (ptp-110) REVERT: H 62 ILE cc_start: 0.9036 (tt) cc_final: 0.8817 (tt) REVERT: H 64 LYS cc_start: 0.8899 (pttm) cc_final: 0.8589 (pttm) REVERT: H 317 MET cc_start: 0.8681 (ttt) cc_final: 0.8337 (ttm) REVERT: H 344 MET cc_start: 0.4799 (ttp) cc_final: 0.3940 (ttp) REVERT: H 387 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7716 (tm-30) REVERT: H 404 LEU cc_start: 0.8937 (mm) cc_final: 0.8533 (mm) outliers start: 3 outliers final: 0 residues processed: 900 average time/residue: 0.3558 time to fit residues: 510.4115 Evaluate side-chains 790 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 790 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 264 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 236 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 270 optimal weight: 0.0570 chunk 219 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 161 optimal weight: 7.9990 chunk 284 optimal weight: 20.0000 chunk 80 optimal weight: 40.0000 overall best weight: 3.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN B 23 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 GLN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 ASN H 225 GLN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 328 GLN H 336 ASN H 405 ASN H 406 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27504 Z= 0.238 Angle : 0.775 12.248 37987 Z= 0.402 Chirality : 0.044 0.270 4428 Planarity : 0.006 0.057 4598 Dihedral : 19.265 167.822 4738 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.08 % Allowed : 2.13 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3216 helix: -0.25 (0.13), residues: 1560 sheet: -1.28 (0.27), residues: 272 loop : -0.91 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 287 HIS 0.017 0.002 HIS E 398 PHE 0.040 0.002 PHE F 159 TYR 0.037 0.002 TYR F 301 ARG 0.030 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 891 time to evaluate : 2.828 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: 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: 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: 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: 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 78 ASN cc_start: 0.8441 (m-40) cc_final: 0.7762 (t0) REVERT: A 206 ASN cc_start: 0.7175 (p0) cc_final: 0.6966 (p0) REVERT: A 208 LYS cc_start: 0.7904 (ptpt) cc_final: 0.7473 (pptt) REVERT: A 225 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7816 (tm-30) REVERT: A 230 ASN cc_start: 0.4722 (p0) cc_final: 0.4407 (p0) REVERT: A 234 ASP cc_start: 0.8616 (m-30) cc_final: 0.8319 (m-30) REVERT: A 315 ARG cc_start: 0.5566 (mpt180) cc_final: 0.5247 (mtp85) REVERT: B 5 ARG cc_start: 0.6768 (ttm170) cc_final: 0.5835 (ttm170) REVERT: B 10 GLU cc_start: 0.8812 (mp0) cc_final: 0.7881 (pp20) REVERT: B 18 LEU cc_start: 0.8045 (pp) cc_final: 0.7320 (pp) REVERT: B 42 MET cc_start: 0.8268 (mtt) cc_final: 0.8064 (mtt) REVERT: B 153 GLN cc_start: 0.8626 (mp10) cc_final: 0.8256 (mp10) REVERT: B 156 LEU cc_start: 0.7848 (mp) cc_final: 0.7478 (mp) REVERT: B 190 ASP cc_start: 0.7479 (p0) cc_final: 0.7100 (p0) REVERT: B 192 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8394 (mp0) REVERT: B 215 GLU cc_start: 0.8889 (mp0) cc_final: 0.8409 (mp0) REVERT: B 261 HIS cc_start: 0.7731 (m-70) cc_final: 0.7385 (m-70) REVERT: B 293 PHE cc_start: 0.7789 (t80) cc_final: 0.7378 (t80) REVERT: B 297 LEU cc_start: 0.7941 (tp) cc_final: 0.5802 (tp) REVERT: B 313 PHE cc_start: 0.6681 (p90) cc_final: 0.6096 (p90) REVERT: B 331 VAL cc_start: 0.8840 (t) cc_final: 0.7874 (t) REVERT: B 332 LEU cc_start: 0.9020 (tp) cc_final: 0.8783 (tp) REVERT: B 341 ASP cc_start: 0.7772 (p0) cc_final: 0.6803 (t0) REVERT: B 387 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7504 (tm-30) REVERT: B 391 LEU cc_start: 0.9306 (mp) cc_final: 0.8772 (mp) REVERT: C 65 MET cc_start: 0.9246 (ttp) cc_final: 0.8291 (tmm) REVERT: C 124 LYS cc_start: 0.7617 (ptpp) cc_final: 0.7127 (ptpp) REVERT: C 126 MET cc_start: 0.8175 (tmm) cc_final: 0.7202 (tpp) REVERT: C 179 MET cc_start: 0.7240 (mmp) cc_final: 0.6527 (mmp) REVERT: C 226 TYR cc_start: 0.8922 (m-10) cc_final: 0.8475 (m-80) REVERT: C 241 GLU cc_start: 0.8546 (mp0) cc_final: 0.8181 (mp0) REVERT: C 250 ASP cc_start: 0.8074 (p0) cc_final: 0.7823 (p0) REVERT: D 84 LEU cc_start: 0.8578 (tp) cc_final: 0.7541 (tp) REVERT: D 153 GLN cc_start: 0.7410 (mp10) cc_final: 0.6786 (mp10) REVERT: D 232 SER cc_start: 0.7982 (p) cc_final: 0.7747 (p) REVERT: D 344 MET cc_start: 0.5950 (ttp) cc_final: 0.5401 (tpt) REVERT: E 89 MET cc_start: 0.6863 (ttt) cc_final: 0.6564 (ppp) REVERT: E 90 LEU cc_start: 0.7436 (mm) cc_final: 0.7043 (mm) REVERT: E 192 GLU cc_start: 0.8449 (mp0) cc_final: 0.7997 (mp0) REVERT: E 250 ASP cc_start: 0.8141 (p0) cc_final: 0.7729 (p0) REVERT: E 398 HIS cc_start: 0.8082 (m-70) cc_final: 0.7694 (m-70) REVERT: F 10 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8209 (pp20) REVERT: F 157 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7530 (mtp180) REVERT: F 195 ARG cc_start: 0.7421 (mtt90) cc_final: 0.6878 (tpp80) REVERT: F 208 LYS cc_start: 0.5400 (mmtt) cc_final: 0.4895 (mmtm) REVERT: F 261 HIS cc_start: 0.7185 (m-70) cc_final: 0.6939 (m-70) REVERT: F 387 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7670 (tm-30) REVERT: F 391 LEU cc_start: 0.9163 (mp) cc_final: 0.8667 (mp) REVERT: G 39 PHE cc_start: 0.4698 (m-80) cc_final: 0.4398 (m-80) REVERT: G 55 ARG cc_start: 0.7231 (mmm-85) cc_final: 0.6829 (mmt90) REVERT: G 65 MET cc_start: 0.8460 (mmp) cc_final: 0.8198 (mmt) REVERT: G 81 SER cc_start: 0.8548 (t) cc_final: 0.7896 (p) REVERT: G 218 MET cc_start: 0.8465 (tmm) cc_final: 0.8212 (tmm) REVERT: G 226 TYR cc_start: 0.8475 (m-10) cc_final: 0.8024 (m-80) REVERT: G 233 LEU cc_start: 0.7595 (mm) cc_final: 0.7320 (mm) REVERT: G 406 GLN cc_start: 0.6565 (tm-30) cc_final: 0.6007 (tm-30) REVERT: H 14 GLN cc_start: 0.7787 (pp30) cc_final: 0.7068 (pp30) REVERT: H 17 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8028 (mm-40) REVERT: H 21 GLN cc_start: 0.9025 (mp-120) cc_final: 0.8675 (mp10) REVERT: H 28 GLU cc_start: 0.8811 (tm-30) cc_final: 0.7766 (tm-30) REVERT: H 29 ILE cc_start: 0.8999 (mt) cc_final: 0.8678 (mt) REVERT: H 32 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7420 (mm-30) REVERT: H 317 MET cc_start: 0.8646 (ttt) cc_final: 0.8238 (ttm) REVERT: H 344 MET cc_start: 0.4589 (ttp) cc_final: 0.3969 (ttp) REVERT: H 387 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7690 (tm-30) REVERT: H 404 LEU cc_start: 0.8975 (mm) cc_final: 0.8607 (mm) outliers start: 2 outliers final: 0 residues processed: 893 average time/residue: 0.3580 time to fit residues: 509.5017 Evaluate side-chains 795 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 795 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 106 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 317 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 ASN G 383 GLN H 70 HIS ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 ASN ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 405 ASN H 406 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27504 Z= 0.219 Angle : 0.749 11.081 37987 Z= 0.388 Chirality : 0.044 0.250 4428 Planarity : 0.005 0.064 4598 Dihedral : 19.075 166.943 4738 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.16 % Allowed : 1.54 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3216 helix: -0.09 (0.13), residues: 1540 sheet: -1.21 (0.27), residues: 272 loop : -0.98 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 287 HIS 0.019 0.002 HIS B 70 PHE 0.042 0.002 PHE C 293 TYR 0.025 0.002 TYR F 143 ARG 0.017 0.001 ARG D 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 894 time to evaluate : 2.881 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.7271 (t) cc_final: 0.6755 (t) REVERT: A 78 ASN cc_start: 0.8441 (m-40) cc_final: 0.7704 (t0) REVERT: A 86 GLU cc_start: 0.7766 (tp30) cc_final: 0.7333 (mm-30) REVERT: A 208 LYS cc_start: 0.8040 (ptpt) cc_final: 0.7674 (ptpt) REVERT: A 225 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7865 (tm-30) REVERT: A 230 ASN cc_start: 0.4674 (p0) cc_final: 0.4381 (p0) REVERT: A 234 ASP cc_start: 0.8648 (m-30) cc_final: 0.8348 (m-30) REVERT: A 315 ARG cc_start: 0.5648 (mpt180) cc_final: 0.5292 (mtp85) REVERT: A 355 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8454 (mt-10) REVERT: A 398 HIS cc_start: 0.7232 (m-70) cc_final: 0.6891 (m-70) REVERT: B 5 ARG cc_start: 0.6771 (ttm170) cc_final: 0.5773 (ttm170) REVERT: B 18 LEU cc_start: 0.7958 (pp) cc_final: 0.7188 (pp) REVERT: B 22 VAL cc_start: 0.8258 (t) cc_final: 0.6872 (t) REVERT: B 42 MET cc_start: 0.8288 (mtt) cc_final: 0.8085 (mtt) REVERT: B 153 GLN cc_start: 0.8585 (mp10) cc_final: 0.8205 (mp10) REVERT: B 156 LEU cc_start: 0.7857 (mp) cc_final: 0.7569 (mp) REVERT: B 192 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8483 (mp0) REVERT: B 215 GLU cc_start: 0.8887 (mp0) cc_final: 0.8396 (mp0) REVERT: B 261 HIS cc_start: 0.7671 (m-70) cc_final: 0.7315 (m-70) REVERT: B 313 PHE cc_start: 0.6596 (p90) cc_final: 0.6078 (p90) REVERT: B 331 VAL cc_start: 0.8841 (t) cc_final: 0.7890 (t) REVERT: B 332 LEU cc_start: 0.9045 (tp) cc_final: 0.8777 (tp) REVERT: B 341 ASP cc_start: 0.7804 (p0) cc_final: 0.6869 (t0) REVERT: B 387 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7455 (tm-30) REVERT: B 391 LEU cc_start: 0.9304 (mp) cc_final: 0.8689 (mp) REVERT: C 65 MET cc_start: 0.9277 (ttp) cc_final: 0.8554 (tmm) REVERT: C 82 ILE cc_start: 0.8459 (pt) cc_final: 0.8066 (pt) REVERT: C 90 LEU cc_start: 0.7087 (tt) cc_final: 0.6269 (mm) REVERT: C 124 LYS cc_start: 0.7428 (ptpp) cc_final: 0.6996 (ptpp) REVERT: C 126 MET cc_start: 0.8112 (tmm) cc_final: 0.7134 (tpp) REVERT: C 179 MET cc_start: 0.7198 (mmp) cc_final: 0.6364 (mmp) REVERT: C 226 TYR cc_start: 0.8883 (m-10) cc_final: 0.8409 (m-80) REVERT: C 241 GLU cc_start: 0.8485 (mp0) cc_final: 0.8118 (mp0) REVERT: C 250 ASP cc_start: 0.8046 (p0) cc_final: 0.7812 (p0) REVERT: C 291 VAL cc_start: 0.6569 (t) cc_final: 0.6357 (t) REVERT: D 84 LEU cc_start: 0.8740 (tp) cc_final: 0.8140 (tp) REVERT: D 153 GLN cc_start: 0.7443 (mp10) cc_final: 0.7011 (mp10) REVERT: D 225 GLN cc_start: 0.8739 (mm110) cc_final: 0.8483 (mm110) REVERT: D 261 HIS cc_start: 0.7604 (m-70) cc_final: 0.7073 (m-70) REVERT: E 89 MET cc_start: 0.6786 (ttt) cc_final: 0.6527 (ppp) REVERT: E 185 ASP cc_start: 0.7867 (m-30) cc_final: 0.7664 (m-30) REVERT: E 250 ASP cc_start: 0.8161 (p0) cc_final: 0.7784 (p0) REVERT: F 10 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8280 (pp20) REVERT: F 25 ASP cc_start: 0.8510 (m-30) cc_final: 0.8291 (m-30) REVERT: F 135 LEU cc_start: 0.9211 (mt) cc_final: 0.8988 (mt) REVERT: F 157 ARG cc_start: 0.7821 (mtm110) cc_final: 0.7532 (mtp180) REVERT: F 195 ARG cc_start: 0.7420 (mtt90) cc_final: 0.6892 (tpp80) REVERT: F 208 LYS cc_start: 0.5477 (mmtt) cc_final: 0.5002 (mmtm) REVERT: F 255 MET cc_start: 0.5533 (mtt) cc_final: 0.5268 (mtt) REVERT: F 261 HIS cc_start: 0.7329 (m-70) cc_final: 0.7059 (m-70) REVERT: F 387 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7620 (tm-30) REVERT: F 391 LEU cc_start: 0.9168 (mp) cc_final: 0.8724 (mp) REVERT: G 39 PHE cc_start: 0.4667 (m-80) cc_final: 0.4320 (m-80) REVERT: G 55 ARG cc_start: 0.7118 (mmm-85) cc_final: 0.6874 (mmt90) REVERT: G 65 MET cc_start: 0.8460 (mmp) cc_final: 0.8203 (mmt) REVERT: G 81 SER cc_start: 0.8577 (t) cc_final: 0.7916 (p) REVERT: G 126 MET cc_start: 0.8378 (tmm) cc_final: 0.8166 (tmm) REVERT: G 218 MET cc_start: 0.8434 (tmm) cc_final: 0.8149 (tmm) REVERT: G 226 TYR cc_start: 0.8457 (m-10) cc_final: 0.7948 (m-80) REVERT: G 237 ARG cc_start: 0.8068 (ptp-170) cc_final: 0.7648 (ptp90) REVERT: G 406 GLN cc_start: 0.6592 (tm-30) cc_final: 0.6278 (tm-30) REVERT: H 14 GLN cc_start: 0.7882 (pp30) cc_final: 0.7168 (pp30) REVERT: H 17 GLN cc_start: 0.8586 (mm-40) cc_final: 0.7884 (mm-40) REVERT: H 21 GLN cc_start: 0.8929 (mp-120) cc_final: 0.8466 (mp10) REVERT: H 28 GLU cc_start: 0.8832 (tm-30) cc_final: 0.7705 (tm-30) REVERT: H 29 ILE cc_start: 0.9016 (mt) cc_final: 0.8673 (mt) REVERT: H 32 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7425 (mm-30) REVERT: H 192 GLU cc_start: 0.8912 (tp30) cc_final: 0.8667 (tp30) REVERT: H 317 MET cc_start: 0.8623 (ttt) cc_final: 0.7690 (tpt) REVERT: H 344 MET cc_start: 0.5074 (ttp) cc_final: 0.4653 (ttp) REVERT: H 387 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7637 (tm-30) REVERT: H 404 LEU cc_start: 0.8865 (mm) cc_final: 0.8546 (mm) outliers start: 4 outliers final: 0 residues processed: 895 average time/residue: 0.3567 time to fit residues: 510.2194 Evaluate side-chains 798 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 798 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 305 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 267 optimal weight: 10.0000 chunk 177 optimal weight: 30.0000 chunk 316 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 GLN E 398 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 ASN ** G 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 400 HIS H 116 GLN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN H 406 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27504 Z= 0.273 Angle : 0.793 13.520 37987 Z= 0.417 Chirality : 0.045 0.343 4428 Planarity : 0.006 0.101 4598 Dihedral : 18.948 166.065 4738 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.08 % Allowed : 1.30 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3216 helix: -0.23 (0.13), residues: 1564 sheet: -1.25 (0.27), residues: 296 loop : -1.04 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP H 267 HIS 0.020 0.002 HIS E 398 PHE 0.046 0.003 PHE E 293 TYR 0.025 0.002 TYR F 143 ARG 0.014 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 875 time to evaluate : 2.834 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8531 (m-40) cc_final: 0.7760 (t0) REVERT: A 208 LYS cc_start: 0.8053 (ptpt) cc_final: 0.7697 (ptpt) REVERT: A 230 ASN cc_start: 0.4543 (p0) cc_final: 0.4260 (p0) REVERT: A 234 ASP cc_start: 0.8690 (m-30) cc_final: 0.8435 (m-30) REVERT: A 355 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8508 (mt-10) REVERT: A 398 HIS cc_start: 0.7339 (m-70) cc_final: 0.6951 (m-70) REVERT: B 5 ARG cc_start: 0.7073 (ttm170) cc_final: 0.6072 (ttm170) REVERT: B 9 ILE cc_start: 0.8972 (pt) cc_final: 0.8724 (pt) REVERT: B 10 GLU cc_start: 0.8823 (mp0) cc_final: 0.7653 (pp20) REVERT: B 18 LEU cc_start: 0.7972 (pp) cc_final: 0.7161 (pp) REVERT: B 22 VAL cc_start: 0.8338 (t) cc_final: 0.6756 (t) REVERT: B 116 GLN cc_start: 0.8669 (tt0) cc_final: 0.8284 (tt0) REVERT: B 156 LEU cc_start: 0.8229 (mp) cc_final: 0.7859 (mp) REVERT: B 215 GLU cc_start: 0.8930 (mp0) cc_final: 0.8448 (mp0) REVERT: B 297 LEU cc_start: 0.8112 (tp) cc_final: 0.6518 (tp) REVERT: B 313 PHE cc_start: 0.6928 (p90) cc_final: 0.6297 (p90) REVERT: B 317 MET cc_start: 0.8037 (tpt) cc_final: 0.7482 (tpt) REVERT: B 331 VAL cc_start: 0.8880 (t) cc_final: 0.7946 (t) REVERT: B 332 LEU cc_start: 0.9059 (tp) cc_final: 0.8810 (tp) REVERT: B 341 ASP cc_start: 0.7684 (p0) cc_final: 0.6398 (m-30) REVERT: B 344 MET cc_start: 0.8380 (ttm) cc_final: 0.7766 (ttm) REVERT: B 383 GLN cc_start: 0.9355 (pm20) cc_final: 0.9034 (pm20) REVERT: B 387 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7437 (tm-30) REVERT: B 391 LEU cc_start: 0.9311 (mp) cc_final: 0.8778 (mp) REVERT: C 124 LYS cc_start: 0.7747 (ptpp) cc_final: 0.7449 (ptpp) REVERT: C 126 MET cc_start: 0.8193 (tmm) cc_final: 0.7188 (tpp) REVERT: C 179 MET cc_start: 0.7145 (mmp) cc_final: 0.6673 (mmp) REVERT: C 226 TYR cc_start: 0.8950 (m-10) cc_final: 0.8497 (m-80) REVERT: C 291 VAL cc_start: 0.6832 (t) cc_final: 0.6626 (t) REVERT: C 335 MET cc_start: 0.8231 (mtm) cc_final: 0.7938 (mtm) REVERT: D 84 LEU cc_start: 0.8753 (tp) cc_final: 0.7755 (tp) REVERT: D 153 GLN cc_start: 0.7491 (mp10) cc_final: 0.7060 (mp10) REVERT: D 261 HIS cc_start: 0.7408 (m-70) cc_final: 0.6664 (m-70) REVERT: D 307 ASP cc_start: 0.6527 (p0) cc_final: 0.6152 (m-30) REVERT: D 328 GLN cc_start: 0.7428 (tp-100) cc_final: 0.7194 (tp-100) REVERT: D 332 LEU cc_start: 0.9161 (tp) cc_final: 0.8850 (tp) REVERT: D 334 GLU cc_start: 0.8711 (tt0) cc_final: 0.8329 (tt0) REVERT: D 344 MET cc_start: 0.5756 (ttp) cc_final: 0.5062 (tpt) REVERT: E 199 MET cc_start: 0.5583 (mmp) cc_final: 0.5051 (tpp) REVERT: E 250 ASP cc_start: 0.8089 (p0) cc_final: 0.7768 (p0) REVERT: F 10 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8295 (pp20) REVERT: F 86 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7004 (mt-10) REVERT: F 157 ARG cc_start: 0.7960 (mtm110) cc_final: 0.7694 (mtp180) REVERT: F 195 ARG cc_start: 0.7319 (mtt90) cc_final: 0.6750 (tpp80) REVERT: F 208 LYS cc_start: 0.5443 (mmtt) cc_final: 0.4303 (mmtm) REVERT: F 234 ASP cc_start: 0.7154 (m-30) cc_final: 0.6950 (m-30) REVERT: F 255 MET cc_start: 0.5412 (mtt) cc_final: 0.5176 (mtt) REVERT: F 261 HIS cc_start: 0.7397 (m-70) cc_final: 0.7053 (m-70) REVERT: F 301 TYR cc_start: 0.7899 (m-80) cc_final: 0.7213 (m-80) REVERT: F 387 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7526 (tm-30) REVERT: F 391 LEU cc_start: 0.9176 (mp) cc_final: 0.8556 (mp) REVERT: G 218 MET cc_start: 0.8421 (tmm) cc_final: 0.8104 (tmm) REVERT: G 226 TYR cc_start: 0.8460 (m-10) cc_final: 0.7987 (m-80) REVERT: G 255 MET cc_start: 0.6129 (ttm) cc_final: 0.4706 (tpt) REVERT: H 14 GLN cc_start: 0.7914 (pp30) cc_final: 0.7197 (pp30) REVERT: H 28 GLU cc_start: 0.8900 (tm-30) cc_final: 0.7721 (tm-30) REVERT: H 29 ILE cc_start: 0.9047 (mt) cc_final: 0.8692 (mt) REVERT: H 32 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7522 (mm-30) REVERT: H 62 ILE cc_start: 0.9212 (tt) cc_final: 0.8985 (tt) REVERT: H 64 LYS cc_start: 0.8969 (pttm) cc_final: 0.8520 (pttm) REVERT: H 159 PHE cc_start: 0.7821 (t80) cc_final: 0.7115 (t80) REVERT: H 192 GLU cc_start: 0.8907 (tp30) cc_final: 0.8688 (tp30) REVERT: H 193 PHE cc_start: 0.8356 (t80) cc_final: 0.8109 (t80) REVERT: H 317 MET cc_start: 0.8559 (ttt) cc_final: 0.7753 (tpt) REVERT: H 320 MET cc_start: 0.6586 (mpp) cc_final: 0.5928 (mpp) REVERT: H 387 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7708 (tm-30) REVERT: H 393 LEU cc_start: 0.8571 (tp) cc_final: 0.8363 (tp) REVERT: H 404 LEU cc_start: 0.8806 (mm) cc_final: 0.8337 (mm) REVERT: H 405 ASN cc_start: 0.5667 (m-40) cc_final: 0.4284 (t0) outliers start: 2 outliers final: 0 residues processed: 876 average time/residue: 0.3640 time to fit residues: 517.2306 Evaluate side-chains 783 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 783 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 195 optimal weight: 0.0870 chunk 126 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 HIS ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 HIS E 342 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27504 Z= 0.239 Angle : 0.787 14.251 37987 Z= 0.408 Chirality : 0.045 0.243 4428 Planarity : 0.006 0.067 4598 Dihedral : 18.815 168.046 4738 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.16 % Allowed : 1.11 % Favored : 98.74 % 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: -0.99 (0.14), residues: 3216 helix: -0.19 (0.13), residues: 1564 sheet: -1.09 (0.28), residues: 280 loop : -0.97 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP C 401 HIS 0.016 0.002 HIS A 398 PHE 0.045 0.003 PHE D 293 TYR 0.024 0.002 TYR H 301 ARG 0.020 0.001 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 868 time to evaluate : 2.938 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 THR cc_start: 0.7872 (t) cc_final: 0.7230 (t) REVERT: A 23 GLN cc_start: 0.8334 (pm20) cc_final: 0.7921 (pm20) REVERT: A 78 ASN cc_start: 0.8532 (m-40) cc_final: 0.7757 (t0) REVERT: A 105 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6787 (p0) REVERT: A 208 LYS cc_start: 0.8129 (ptpt) cc_final: 0.7729 (ptpt) REVERT: A 234 ASP cc_start: 0.8706 (m-30) cc_final: 0.8432 (m-30) REVERT: A 348 ILE cc_start: 0.9029 (mm) cc_final: 0.8808 (mm) REVERT: A 355 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8463 (mt-10) REVERT: A 398 HIS cc_start: 0.7366 (m-70) cc_final: 0.6362 (m-70) REVERT: A 400 HIS cc_start: 0.7602 (m90) cc_final: 0.7312 (m90) REVERT: B 5 ARG cc_start: 0.6978 (ttm170) cc_final: 0.6153 (tpp80) REVERT: B 10 GLU cc_start: 0.8800 (mp0) cc_final: 0.7617 (pp20) REVERT: B 116 GLN cc_start: 0.8610 (tt0) cc_final: 0.8259 (tt0) REVERT: B 156 LEU cc_start: 0.8019 (mp) cc_final: 0.7724 (mp) REVERT: B 192 GLU cc_start: 0.8439 (mp0) cc_final: 0.7931 (mp0) REVERT: B 215 GLU cc_start: 0.8875 (mp0) cc_final: 0.8402 (mp0) REVERT: B 297 LEU cc_start: 0.8083 (tp) cc_final: 0.6641 (tp) REVERT: B 313 PHE cc_start: 0.6706 (p90) cc_final: 0.6187 (p90) REVERT: B 331 VAL cc_start: 0.8802 (t) cc_final: 0.7827 (t) REVERT: B 332 LEU cc_start: 0.9065 (tp) cc_final: 0.8846 (tp) REVERT: B 341 ASP cc_start: 0.7678 (p0) cc_final: 0.6364 (m-30) REVERT: B 344 MET cc_start: 0.8344 (ttm) cc_final: 0.7839 (ttm) REVERT: B 383 GLN cc_start: 0.9340 (pm20) cc_final: 0.9101 (pm20) REVERT: B 387 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7440 (tm-30) REVERT: B 391 LEU cc_start: 0.9298 (mp) cc_final: 0.8634 (mp) REVERT: C 90 LEU cc_start: 0.7184 (tt) cc_final: 0.6528 (mm) REVERT: C 124 LYS cc_start: 0.7520 (ptpp) cc_final: 0.7136 (ptpp) REVERT: C 126 MET cc_start: 0.8011 (tmm) cc_final: 0.7051 (tpp) REVERT: C 179 MET cc_start: 0.7189 (mmp) cc_final: 0.6371 (mmp) REVERT: C 226 TYR cc_start: 0.8927 (m-10) cc_final: 0.8474 (m-80) REVERT: C 241 GLU cc_start: 0.8512 (mp0) cc_final: 0.8141 (mp0) REVERT: C 291 VAL cc_start: 0.6537 (t) cc_final: 0.6310 (t) REVERT: D 84 LEU cc_start: 0.8708 (tp) cc_final: 0.8110 (tp) REVERT: D 153 GLN cc_start: 0.7416 (mp10) cc_final: 0.6958 (mp10) REVERT: D 261 HIS cc_start: 0.7380 (m-70) cc_final: 0.6617 (m-70) REVERT: D 328 GLN cc_start: 0.7301 (tp-100) cc_final: 0.7081 (tp-100) REVERT: D 332 LEU cc_start: 0.9159 (tp) cc_final: 0.8939 (tp) REVERT: D 334 GLU cc_start: 0.8683 (tt0) cc_final: 0.8245 (tt0) REVERT: D 344 MET cc_start: 0.5703 (ttp) cc_final: 0.5301 (tpt) REVERT: E 199 MET cc_start: 0.5553 (mmp) cc_final: 0.5078 (tpp) REVERT: E 250 ASP cc_start: 0.7996 (p0) cc_final: 0.7727 (p0) REVERT: E 264 PRO cc_start: 0.8567 (Cg_exo) cc_final: 0.8210 (Cg_endo) REVERT: F 10 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8252 (pp20) REVERT: F 20 GLN cc_start: 0.7866 (mt0) cc_final: 0.7374 (mp10) REVERT: F 25 ASP cc_start: 0.8529 (m-30) cc_final: 0.8318 (m-30) REVERT: F 86 GLU cc_start: 0.8054 (mt-10) cc_final: 0.6902 (mt-10) REVERT: F 195 ARG cc_start: 0.7401 (mtt90) cc_final: 0.6850 (tpp80) REVERT: F 255 MET cc_start: 0.5409 (mtt) cc_final: 0.5182 (mtt) REVERT: F 261 HIS cc_start: 0.7288 (m-70) cc_final: 0.6937 (m-70) REVERT: F 301 TYR cc_start: 0.7843 (m-80) cc_final: 0.7213 (m-80) REVERT: F 387 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7490 (tm-30) REVERT: F 391 LEU cc_start: 0.9165 (mp) cc_final: 0.8536 (mp) REVERT: G 218 MET cc_start: 0.8438 (tmm) cc_final: 0.8096 (tmm) REVERT: G 226 TYR cc_start: 0.8412 (m-10) cc_final: 0.7940 (m-80) REVERT: G 255 MET cc_start: 0.5953 (ttm) cc_final: 0.4665 (tpt) REVERT: G 301 TYR cc_start: 0.7964 (m-80) cc_final: 0.7711 (m-80) REVERT: G 320 MET cc_start: 0.6500 (tpt) cc_final: 0.6247 (tpt) REVERT: G 406 GLN cc_start: 0.6888 (tm-30) cc_final: 0.6386 (tm-30) REVERT: H 14 GLN cc_start: 0.7929 (pp30) cc_final: 0.7222 (pp30) REVERT: H 28 GLU cc_start: 0.8843 (tm-30) cc_final: 0.7643 (tm-30) REVERT: H 29 ILE cc_start: 0.9033 (mt) cc_final: 0.8702 (mt) REVERT: H 32 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7526 (mm-30) REVERT: H 62 ILE cc_start: 0.9206 (tt) cc_final: 0.8947 (tt) REVERT: H 64 LYS cc_start: 0.9009 (pttm) cc_final: 0.8578 (pttm) REVERT: H 159 PHE cc_start: 0.7688 (t80) cc_final: 0.6875 (t80) REVERT: H 192 GLU cc_start: 0.8904 (tp30) cc_final: 0.8674 (tp30) REVERT: H 320 MET cc_start: 0.6454 (mpp) cc_final: 0.5795 (mpp) REVERT: H 383 GLN cc_start: 0.8796 (pm20) cc_final: 0.8551 (pm20) REVERT: H 387 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7606 (tm-30) REVERT: H 404 LEU cc_start: 0.8852 (mm) cc_final: 0.8514 (mm) outliers start: 4 outliers final: 0 residues processed: 870 average time/residue: 0.3434 time to fit residues: 483.4581 Evaluate side-chains 768 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 767 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 287 optimal weight: 20.0000 chunk 302 optimal weight: 50.0000 chunk 276 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 266 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 GLN E 398 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 HIS ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 27504 Z= 0.320 Angle : 0.836 13.550 37987 Z= 0.438 Chirality : 0.047 0.302 4428 Planarity : 0.006 0.076 4598 Dihedral : 18.925 166.300 4738 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 28.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.08 % Allowed : 0.91 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3216 helix: -0.38 (0.12), residues: 1564 sheet: -1.26 (0.28), residues: 276 loop : -1.10 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP C 401 HIS 0.018 0.002 HIS E 398 PHE 0.041 0.003 PHE F 159 TYR 0.018 0.002 TYR H 301 ARG 0.014 0.001 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 867 time to evaluate : 2.862 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: 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: 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: 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 19 THR cc_start: 0.7878 (t) cc_final: 0.7248 (t) REVERT: A 23 GLN cc_start: 0.8272 (pm20) cc_final: 0.7883 (pm20) REVERT: A 65 MET cc_start: 0.6947 (tmm) cc_final: 0.6726 (tmm) REVERT: A 78 ASN cc_start: 0.8628 (m-40) cc_final: 0.7834 (t0) REVERT: A 179 MET cc_start: 0.9461 (mpp) cc_final: 0.8839 (mpp) REVERT: A 208 LYS cc_start: 0.8128 (ptpt) cc_final: 0.7853 (ptpt) REVERT: A 226 TYR cc_start: 0.8561 (m-10) cc_final: 0.8201 (m-80) REVERT: A 234 ASP cc_start: 0.8766 (m-30) cc_final: 0.8500 (m-30) REVERT: A 291 VAL cc_start: 0.7628 (t) cc_final: 0.7091 (t) REVERT: A 355 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8623 (mt-10) REVERT: B 5 ARG cc_start: 0.7321 (ttm170) cc_final: 0.6340 (tpp80) REVERT: B 10 GLU cc_start: 0.8867 (mp0) cc_final: 0.7626 (pp20) REVERT: B 156 LEU cc_start: 0.8334 (mp) cc_final: 0.7986 (mp) REVERT: B 192 GLU cc_start: 0.8597 (mp0) cc_final: 0.8232 (mp0) REVERT: B 215 GLU cc_start: 0.8960 (mp0) cc_final: 0.8515 (mp0) REVERT: B 297 LEU cc_start: 0.8204 (tp) cc_final: 0.6954 (tp) REVERT: B 301 TYR cc_start: 0.8094 (m-10) cc_final: 0.7806 (m-10) REVERT: B 313 PHE cc_start: 0.6960 (p90) cc_final: 0.6472 (p90) REVERT: B 331 VAL cc_start: 0.8891 (t) cc_final: 0.8015 (t) REVERT: B 332 LEU cc_start: 0.9092 (tp) cc_final: 0.8879 (tp) REVERT: B 341 ASP cc_start: 0.7349 (p0) cc_final: 0.6134 (m-30) REVERT: B 344 MET cc_start: 0.8282 (ttm) cc_final: 0.7759 (ttm) REVERT: B 383 GLN cc_start: 0.9411 (pm20) cc_final: 0.9036 (pm20) REVERT: B 387 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7471 (tm-30) REVERT: B 391 LEU cc_start: 0.9307 (mp) cc_final: 0.8737 (mp) REVERT: C 124 LYS cc_start: 0.7890 (ptpp) cc_final: 0.7625 (ptpp) REVERT: C 126 MET cc_start: 0.8207 (tmm) cc_final: 0.7249 (tpp) REVERT: C 179 MET cc_start: 0.6989 (mmp) cc_final: 0.6528 (mmp) REVERT: C 195 ARG cc_start: 0.7208 (mpp-170) cc_final: 0.6953 (mpp-170) REVERT: C 226 TYR cc_start: 0.9041 (m-10) cc_final: 0.8619 (m-80) REVERT: C 291 VAL cc_start: 0.6892 (t) cc_final: 0.6608 (t) REVERT: C 386 VAL cc_start: 0.8922 (t) cc_final: 0.8721 (p) REVERT: D 84 LEU cc_start: 0.8891 (tp) cc_final: 0.7916 (tp) REVERT: D 85 SER cc_start: 0.8577 (t) cc_final: 0.8214 (m) REVERT: D 153 GLN cc_start: 0.7514 (mp10) cc_final: 0.7050 (mp10) REVERT: D 261 HIS cc_start: 0.7405 (m-70) cc_final: 0.6590 (m-70) REVERT: D 307 ASP cc_start: 0.6767 (p0) cc_final: 0.6370 (m-30) REVERT: D 332 LEU cc_start: 0.9254 (tp) cc_final: 0.8965 (tp) REVERT: D 334 GLU cc_start: 0.8746 (tt0) cc_final: 0.8540 (tt0) REVERT: D 344 MET cc_start: 0.5979 (ttp) cc_final: 0.5471 (tpt) REVERT: E 199 MET cc_start: 0.5869 (mmp) cc_final: 0.5330 (tpp) REVERT: E 250 ASP cc_start: 0.8066 (p0) cc_final: 0.7802 (p0) REVERT: E 363 THR cc_start: 0.8424 (m) cc_final: 0.8193 (m) REVERT: E 398 HIS cc_start: 0.8320 (m90) cc_final: 0.8064 (m90) REVERT: F 78 ASN cc_start: 0.7353 (t0) cc_final: 0.7149 (t0) REVERT: F 86 GLU cc_start: 0.8092 (mt-10) cc_final: 0.6857 (mt-10) REVERT: F 139 LEU cc_start: 0.9110 (mp) cc_final: 0.8879 (mp) REVERT: F 157 ARG cc_start: 0.6948 (ttp-110) cc_final: 0.6014 (mtp180) REVERT: F 192 GLU cc_start: 0.8585 (pt0) cc_final: 0.8274 (pm20) REVERT: F 234 ASP cc_start: 0.7174 (m-30) cc_final: 0.6943 (m-30) REVERT: F 255 MET cc_start: 0.5467 (mtt) cc_final: 0.5258 (mtt) REVERT: F 261 HIS cc_start: 0.7409 (m-70) cc_final: 0.6995 (m-70) REVERT: F 301 TYR cc_start: 0.7971 (m-80) cc_final: 0.7275 (m-80) REVERT: F 331 VAL cc_start: 0.9129 (t) cc_final: 0.8639 (t) REVERT: F 381 THR cc_start: 0.9373 (p) cc_final: 0.9032 (p) REVERT: F 383 GLN cc_start: 0.9066 (pm20) cc_final: 0.8581 (pm20) REVERT: F 384 ASP cc_start: 0.8674 (m-30) cc_final: 0.8360 (m-30) REVERT: F 387 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7537 (tm-30) REVERT: F 391 LEU cc_start: 0.9204 (mp) cc_final: 0.8603 (mp) REVERT: F 401 TRP cc_start: 0.7062 (t60) cc_final: 0.6811 (t60) REVERT: G 218 MET cc_start: 0.8447 (tmm) cc_final: 0.8067 (tmm) REVERT: G 226 TYR cc_start: 0.8411 (m-10) cc_final: 0.7967 (m-80) REVERT: G 301 TYR cc_start: 0.8282 (m-80) cc_final: 0.7830 (m-80) REVERT: G 320 MET cc_start: 0.7184 (tpt) cc_final: 0.6976 (tpt) REVERT: G 400 HIS cc_start: 0.8350 (m-70) cc_final: 0.8117 (m-70) REVERT: H 14 GLN cc_start: 0.8034 (pp30) cc_final: 0.7299 (pp30) REVERT: H 28 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8233 (tm-30) REVERT: H 29 ILE cc_start: 0.9031 (mt) cc_final: 0.8686 (mt) REVERT: H 159 PHE cc_start: 0.7807 (t80) cc_final: 0.7195 (t80) REVERT: H 192 GLU cc_start: 0.8903 (tp30) cc_final: 0.8703 (tp30) REVERT: H 193 PHE cc_start: 0.8279 (t80) cc_final: 0.8044 (t80) REVERT: H 320 MET cc_start: 0.6755 (mpp) cc_final: 0.5912 (mpp) REVERT: H 383 GLN cc_start: 0.8921 (pm20) cc_final: 0.8622 (pm20) REVERT: H 387 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7260 (tm-30) REVERT: H 398 HIS cc_start: 0.7785 (m-70) cc_final: 0.7225 (m-70) REVERT: H 404 LEU cc_start: 0.9006 (mm) cc_final: 0.8648 (mm) outliers start: 2 outliers final: 0 residues processed: 868 average time/residue: 0.3484 time to fit residues: 490.1344 Evaluate side-chains 776 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 776 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 193 optimal weight: 9.9990 chunk 311 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 147 optimal weight: 30.0000 chunk 216 optimal weight: 0.7980 chunk 326 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 260 optimal weight: 0.0040 chunk 27 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 ASN E 342 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 HIS ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 HIS G 292 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27504 Z= 0.233 Angle : 0.807 13.578 37987 Z= 0.417 Chirality : 0.046 0.249 4428 Planarity : 0.006 0.063 4598 Dihedral : 18.730 170.705 4738 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.16 % Allowed : 0.20 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3216 helix: -0.39 (0.12), residues: 1600 sheet: -0.87 (0.29), residues: 272 loop : -1.27 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP C 401 HIS 0.013 0.002 HIS C 398 PHE 0.047 0.003 PHE D 293 TYR 0.025 0.002 TYR H 301 ARG 0.017 0.001 ARG E 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 856 time to evaluate : 2.767 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: 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: 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: 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 20 GLN cc_start: 0.9070 (mp10) cc_final: 0.8858 (pm20) REVERT: A 65 MET cc_start: 0.6922 (tmm) cc_final: 0.6701 (tmm) REVERT: A 78 ASN cc_start: 0.8505 (m-40) cc_final: 0.7787 (t0) REVERT: A 208 LYS cc_start: 0.8094 (ptpt) cc_final: 0.7750 (ptpt) REVERT: A 234 ASP cc_start: 0.8788 (m-30) cc_final: 0.8471 (m-30) REVERT: A 355 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8544 (mt-10) REVERT: A 394 GLU cc_start: 0.7264 (pp20) cc_final: 0.6776 (pp20) REVERT: A 398 HIS cc_start: 0.7661 (m-70) cc_final: 0.7035 (m-70) REVERT: B 5 ARG cc_start: 0.7065 (ttm170) cc_final: 0.6149 (tpp80) REVERT: B 10 GLU cc_start: 0.8783 (mp0) cc_final: 0.7591 (pp20) REVERT: B 156 LEU cc_start: 0.8154 (mp) cc_final: 0.7834 (mp) REVERT: B 192 GLU cc_start: 0.8588 (mp0) cc_final: 0.7937 (mp0) REVERT: B 215 GLU cc_start: 0.8887 (mp0) cc_final: 0.8458 (mp0) REVERT: B 297 LEU cc_start: 0.8043 (tp) cc_final: 0.6734 (tp) REVERT: B 313 PHE cc_start: 0.6747 (p90) cc_final: 0.6186 (p90) REVERT: B 317 MET cc_start: 0.8028 (tpt) cc_final: 0.7242 (tpt) REVERT: B 331 VAL cc_start: 0.8755 (t) cc_final: 0.7769 (t) REVERT: B 332 LEU cc_start: 0.9080 (tp) cc_final: 0.8877 (tp) REVERT: B 341 ASP cc_start: 0.7700 (p0) cc_final: 0.6579 (m-30) REVERT: B 344 MET cc_start: 0.8131 (ttm) cc_final: 0.7349 (ttm) REVERT: B 383 GLN cc_start: 0.9321 (pm20) cc_final: 0.9111 (pm20) REVERT: B 387 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 391 LEU cc_start: 0.9225 (mp) cc_final: 0.8617 (mp) REVERT: C 124 LYS cc_start: 0.7428 (ptpp) cc_final: 0.7048 (ptpp) REVERT: C 126 MET cc_start: 0.7910 (tmm) cc_final: 0.6983 (tpp) REVERT: C 179 MET cc_start: 0.6994 (mmp) cc_final: 0.6231 (mmm) REVERT: C 226 TYR cc_start: 0.9144 (m-10) cc_final: 0.8701 (m-80) REVERT: C 386 VAL cc_start: 0.8917 (t) cc_final: 0.8695 (p) REVERT: D 84 LEU cc_start: 0.8916 (tp) cc_final: 0.8022 (tp) REVERT: D 153 GLN cc_start: 0.7264 (mp10) cc_final: 0.6839 (mp10) REVERT: D 261 HIS cc_start: 0.7313 (m-70) cc_final: 0.6380 (m-70) REVERT: D 332 LEU cc_start: 0.9182 (tp) cc_final: 0.8872 (tp) REVERT: D 334 GLU cc_start: 0.8662 (tt0) cc_final: 0.8352 (tt0) REVERT: D 344 MET cc_start: 0.5783 (ttp) cc_final: 0.5099 (tpt) REVERT: E 126 MET cc_start: 0.8387 (tmm) cc_final: 0.8162 (tmm) REVERT: E 185 ASP cc_start: 0.7934 (m-30) cc_final: 0.7711 (m-30) REVERT: E 199 MET cc_start: 0.5555 (mmp) cc_final: 0.5118 (tpp) REVERT: E 264 PRO cc_start: 0.8631 (Cg_exo) cc_final: 0.8294 (Cg_endo) REVERT: F 10 GLU cc_start: 0.8737 (mm-30) cc_final: 0.7980 (pp20) REVERT: F 32 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7723 (mt-10) REVERT: F 78 ASN cc_start: 0.7389 (t160) cc_final: 0.7088 (t0) REVERT: F 86 GLU cc_start: 0.7877 (mt-10) cc_final: 0.6822 (mt-10) REVERT: F 139 LEU cc_start: 0.9054 (mp) cc_final: 0.8842 (mp) REVERT: F 157 ARG cc_start: 0.6689 (ttp-110) cc_final: 0.5915 (mtp180) REVERT: F 192 GLU cc_start: 0.8582 (pt0) cc_final: 0.8252 (pm20) REVERT: F 195 ARG cc_start: 0.7371 (mtt90) cc_final: 0.6826 (tpp80) REVERT: F 234 ASP cc_start: 0.7042 (m-30) cc_final: 0.6793 (m-30) REVERT: F 255 MET cc_start: 0.5520 (mtt) cc_final: 0.5255 (mtt) REVERT: F 261 HIS cc_start: 0.7219 (m-70) cc_final: 0.6903 (m-70) REVERT: F 301 TYR cc_start: 0.7786 (m-80) cc_final: 0.7576 (m-80) REVERT: F 383 GLN cc_start: 0.8993 (pm20) cc_final: 0.8647 (pm20) REVERT: F 387 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7558 (tm-30) REVERT: F 391 LEU cc_start: 0.9259 (mp) cc_final: 0.8641 (mp) REVERT: G 218 MET cc_start: 0.8461 (tmm) cc_final: 0.8096 (tmm) REVERT: G 226 TYR cc_start: 0.8392 (m-10) cc_final: 0.7923 (m-80) REVERT: G 364 VAL cc_start: 0.9412 (m) cc_final: 0.9162 (p) REVERT: G 400 HIS cc_start: 0.8191 (m-70) cc_final: 0.7977 (m-70) REVERT: H 14 GLN cc_start: 0.8051 (pp30) cc_final: 0.7304 (pp30) REVERT: H 28 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8152 (tm-30) REVERT: H 29 ILE cc_start: 0.9071 (mt) cc_final: 0.8728 (mt) REVERT: H 62 ILE cc_start: 0.9232 (tt) cc_final: 0.8999 (tt) REVERT: H 159 PHE cc_start: 0.7554 (t80) cc_final: 0.6807 (t80) REVERT: H 193 PHE cc_start: 0.8203 (t80) cc_final: 0.7994 (t80) REVERT: H 317 MET cc_start: 0.8048 (tpt) cc_final: 0.7836 (ttm) REVERT: H 320 MET cc_start: 0.6572 (mpp) cc_final: 0.5864 (mpp) REVERT: H 387 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7759 (tm-30) REVERT: H 404 LEU cc_start: 0.9030 (mm) cc_final: 0.8622 (mm) outliers start: 4 outliers final: 0 residues processed: 858 average time/residue: 0.3515 time to fit residues: 486.5051 Evaluate side-chains 765 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 765 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 206 optimal weight: 9.9990 chunk 277 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 260 optimal weight: 0.0870 chunk 109 optimal weight: 4.9990 chunk 267 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 48 optimal weight: 30.0000 overall best weight: 2.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN E 342 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 383 GLN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 398 HIS H 406 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.213246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.173747 restraints weight = 184166.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.183690 restraints weight = 94713.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.189685 restraints weight = 56787.305| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4227 r_free = 0.4227 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4227 r_free = 0.4227 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 27504 Z= 0.236 Angle : 0.795 12.351 37987 Z= 0.414 Chirality : 0.047 0.606 4428 Planarity : 0.006 0.059 4598 Dihedral : 18.629 170.401 4738 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.76 % 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: -1.16 (0.14), residues: 3216 helix: -0.25 (0.13), residues: 1564 sheet: -0.76 (0.30), residues: 264 loop : -1.28 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP H 401 HIS 0.019 0.002 HIS E 398 PHE 0.051 0.003 PHE F 159 TYR 0.023 0.002 TYR H 301 ARG 0.016 0.001 ARG E 26 =============================================================================== Job complete usr+sys time: 8348.25 seconds wall clock time: 149 minutes 18.75 seconds (8958.75 seconds total)