Starting phenix.real_space_refine on Mon Mar 11 01:33:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/03_2024/8ble_16108_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/03_2024/8ble_16108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/03_2024/8ble_16108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/03_2024/8ble_16108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/03_2024/8ble_16108_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/03_2024/8ble_16108_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 280 5.16 5 C 33754 2.51 5 N 9408 2.21 5 O 10990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 359": "OD1" <-> "OD2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 359": "OD1" <-> "OD2" Residue "F TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 83": "OD1" <-> "OD2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 121": "OD1" <-> "OD2" Residue "K TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 83": "OD1" <-> "OD2" Residue "M GLU 172": "OE1" <-> "OE2" Residue "M TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 359": "OD1" <-> "OD2" Residue "M TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 54474 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.59, per 1000 atoms: 0.38 Number of scatterers: 54474 At special positions: 0 Unit cell: (152.64, 152.64, 160.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 280 16.00 P 42 15.00 O 10990 8.00 N 9408 7.00 C 33754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.63 Conformation dependent library (CDL) restraints added in 7.8 seconds 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 280 helices and 93 sheets defined 53.3% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.57 Creating SS restraints... Processing helix chain 'A' and resid 10 through 30 removed outlier: 4.847A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 85 Processing helix chain 'A' and resid 89 through 109 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 231 through 243 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 282 through 296 Processing helix chain 'A' and resid 339 through 354 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 386 through 408 Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 434 through 447 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 497 through 515 Processing helix chain 'B' and resid 10 through 30 removed outlier: 4.843A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 65 through 85 Processing helix chain 'B' and resid 89 through 109 Processing helix chain 'B' and resid 113 through 134 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 156 through 168 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 231 through 243 Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 339 through 354 Processing helix chain 'B' and resid 359 through 374 Processing helix chain 'B' and resid 386 through 408 Processing helix chain 'B' and resid 417 through 424 Processing helix chain 'B' and resid 434 through 447 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 462 through 471 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'C' and resid 10 through 30 removed outlier: 4.861A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 65 through 84 Processing helix chain 'C' and resid 89 through 109 Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 156 through 168 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 231 through 243 Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 282 through 296 Processing helix chain 'C' and resid 339 through 354 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 408 Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 434 through 447 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 462 through 471 Processing helix chain 'C' and resid 488 through 491 No H-bonds generated for 'chain 'C' and resid 488 through 491' Processing helix chain 'C' and resid 497 through 515 Processing helix chain 'D' and resid 10 through 30 removed outlier: 4.861A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 65 through 85 Processing helix chain 'D' and resid 89 through 108 Processing helix chain 'D' and resid 113 through 134 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 231 through 243 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 282 through 296 Processing helix chain 'D' and resid 339 through 354 Processing helix chain 'D' and resid 359 through 374 Processing helix chain 'D' and resid 386 through 408 Processing helix chain 'D' and resid 417 through 424 Processing helix chain 'D' and resid 434 through 447 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 462 through 471 Processing helix chain 'D' and resid 488 through 491 No H-bonds generated for 'chain 'D' and resid 488 through 491' Processing helix chain 'D' and resid 497 through 515 Processing helix chain 'E' and resid 10 through 30 removed outlier: 4.907A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 65 through 85 Processing helix chain 'E' and resid 89 through 109 Processing helix chain 'E' and resid 113 through 134 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 156 through 169 Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 231 through 243 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 282 through 296 Processing helix chain 'E' and resid 339 through 355 Processing helix chain 'E' and resid 359 through 374 Processing helix chain 'E' and resid 386 through 408 Processing helix chain 'E' and resid 417 through 424 Processing helix chain 'E' and resid 434 through 447 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 462 through 471 Processing helix chain 'E' and resid 488 through 491 No H-bonds generated for 'chain 'E' and resid 488 through 491' Processing helix chain 'E' and resid 497 through 515 Processing helix chain 'F' and resid 10 through 30 removed outlier: 4.861A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 65 through 85 Processing helix chain 'F' and resid 89 through 108 Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 156 through 169 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 231 through 243 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 256 through 268 Processing helix chain 'F' and resid 282 through 296 Processing helix chain 'F' and resid 339 through 354 Processing helix chain 'F' and resid 359 through 374 Processing helix chain 'F' and resid 386 through 408 Processing helix chain 'F' and resid 417 through 424 Processing helix chain 'F' and resid 434 through 447 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 462 through 471 Processing helix chain 'F' and resid 488 through 491 No H-bonds generated for 'chain 'F' and resid 488 through 491' Processing helix chain 'F' and resid 497 through 515 Processing helix chain 'G' and resid 10 through 30 removed outlier: 4.896A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 Processing helix chain 'G' and resid 65 through 84 Processing helix chain 'G' and resid 89 through 109 Processing helix chain 'G' and resid 113 through 134 Processing helix chain 'G' and resid 141 through 151 Processing helix chain 'G' and resid 156 through 168 Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 231 through 243 Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 256 through 268 Processing helix chain 'G' and resid 282 through 296 Processing helix chain 'G' and resid 339 through 354 Processing helix chain 'G' and resid 359 through 374 Processing helix chain 'G' and resid 386 through 408 Processing helix chain 'G' and resid 417 through 424 Processing helix chain 'G' and resid 434 through 447 Processing helix chain 'G' and resid 449 through 458 Processing helix chain 'G' and resid 462 through 471 Processing helix chain 'G' and resid 488 through 491 No H-bonds generated for 'chain 'G' and resid 488 through 491' Processing helix chain 'G' and resid 497 through 515 Processing helix chain 'H' and resid 10 through 30 removed outlier: 4.817A pdb=" N THR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 65 through 85 Processing helix chain 'H' and resid 89 through 108 Processing helix chain 'H' and resid 113 through 134 Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 156 through 169 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 231 through 243 Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 256 through 268 Processing helix chain 'H' and resid 282 through 296 Processing helix chain 'H' and resid 339 through 354 Processing helix chain 'H' and resid 359 through 374 Processing helix chain 'H' and resid 386 through 408 Processing helix chain 'H' and resid 417 through 424 Processing helix chain 'H' and resid 434 through 447 Processing helix chain 'H' and resid 449 through 458 Processing helix chain 'H' and resid 462 through 471 Processing helix chain 'H' and resid 488 through 491 No H-bonds generated for 'chain 'H' and resid 488 through 491' Processing helix chain 'H' and resid 497 through 515 Processing helix chain 'I' and resid 10 through 30 removed outlier: 4.852A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 65 through 85 Processing helix chain 'I' and resid 89 through 109 Processing helix chain 'I' and resid 113 through 134 Processing helix chain 'I' and resid 141 through 151 Processing helix chain 'I' and resid 156 through 168 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 231 through 243 Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 256 through 268 Processing helix chain 'I' and resid 282 through 296 Processing helix chain 'I' and resid 339 through 355 Processing helix chain 'I' and resid 359 through 374 Processing helix chain 'I' and resid 386 through 408 Processing helix chain 'I' and resid 417 through 424 Processing helix chain 'I' and resid 434 through 447 Processing helix chain 'I' and resid 449 through 458 Processing helix chain 'I' and resid 462 through 471 Processing helix chain 'I' and resid 488 through 491 No H-bonds generated for 'chain 'I' and resid 488 through 491' Processing helix chain 'I' and resid 497 through 515 Processing helix chain 'J' and resid 10 through 30 removed outlier: 4.840A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 65 through 85 Processing helix chain 'J' and resid 89 through 109 Processing helix chain 'J' and resid 113 through 134 Processing helix chain 'J' and resid 141 through 151 Processing helix chain 'J' and resid 156 through 169 Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 231 through 243 Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 256 through 268 Processing helix chain 'J' and resid 282 through 296 Processing helix chain 'J' and resid 339 through 354 Processing helix chain 'J' and resid 359 through 374 Processing helix chain 'J' and resid 386 through 408 Processing helix chain 'J' and resid 417 through 424 Processing helix chain 'J' and resid 434 through 447 Processing helix chain 'J' and resid 449 through 458 Processing helix chain 'J' and resid 462 through 471 Processing helix chain 'J' and resid 488 through 491 No H-bonds generated for 'chain 'J' and resid 488 through 491' Processing helix chain 'J' and resid 497 through 515 Processing helix chain 'K' and resid 10 through 30 removed outlier: 4.801A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 65 through 85 Processing helix chain 'K' and resid 89 through 108 Processing helix chain 'K' and resid 113 through 134 Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 156 through 168 Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 231 through 243 Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 256 through 268 Processing helix chain 'K' and resid 282 through 296 Processing helix chain 'K' and resid 339 through 354 Processing helix chain 'K' and resid 359 through 374 Processing helix chain 'K' and resid 386 through 408 Processing helix chain 'K' and resid 417 through 424 Processing helix chain 'K' and resid 434 through 447 Processing helix chain 'K' and resid 449 through 458 Processing helix chain 'K' and resid 462 through 471 Processing helix chain 'K' and resid 488 through 491 No H-bonds generated for 'chain 'K' and resid 488 through 491' Processing helix chain 'K' and resid 497 through 515 Processing helix chain 'L' and resid 10 through 30 removed outlier: 4.857A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 65 through 85 Processing helix chain 'L' and resid 89 through 108 Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 141 through 151 Processing helix chain 'L' and resid 156 through 169 Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 231 through 243 Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 256 through 268 Processing helix chain 'L' and resid 282 through 296 Processing helix chain 'L' and resid 339 through 355 Processing helix chain 'L' and resid 359 through 374 Processing helix chain 'L' and resid 386 through 408 Processing helix chain 'L' and resid 417 through 424 Processing helix chain 'L' and resid 434 through 447 Processing helix chain 'L' and resid 449 through 458 Processing helix chain 'L' and resid 462 through 471 Processing helix chain 'L' and resid 488 through 491 No H-bonds generated for 'chain 'L' and resid 488 through 491' Processing helix chain 'L' and resid 497 through 515 Processing helix chain 'M' and resid 10 through 30 removed outlier: 4.871A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 65 through 85 Processing helix chain 'M' and resid 89 through 108 Processing helix chain 'M' and resid 113 through 134 Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'M' and resid 156 through 169 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 231 through 243 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 256 through 268 Processing helix chain 'M' and resid 282 through 296 Processing helix chain 'M' and resid 339 through 354 Processing helix chain 'M' and resid 359 through 374 Processing helix chain 'M' and resid 386 through 408 Processing helix chain 'M' and resid 417 through 424 Processing helix chain 'M' and resid 434 through 447 Processing helix chain 'M' and resid 449 through 458 Processing helix chain 'M' and resid 462 through 471 Processing helix chain 'M' and resid 488 through 491 No H-bonds generated for 'chain 'M' and resid 488 through 491' Processing helix chain 'M' and resid 497 through 515 Processing helix chain 'N' and resid 10 through 30 removed outlier: 4.913A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 59 Processing helix chain 'N' and resid 65 through 85 Processing helix chain 'N' and resid 89 through 108 Processing helix chain 'N' and resid 113 through 134 Processing helix chain 'N' and resid 141 through 151 Processing helix chain 'N' and resid 156 through 168 Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 231 through 243 Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 256 through 268 Processing helix chain 'N' and resid 282 through 296 Processing helix chain 'N' and resid 339 through 354 Processing helix chain 'N' and resid 359 through 374 Processing helix chain 'N' and resid 386 through 408 Processing helix chain 'N' and resid 417 through 424 Processing helix chain 'N' and resid 434 through 447 Processing helix chain 'N' and resid 449 through 458 Processing helix chain 'N' and resid 462 through 471 Processing helix chain 'N' and resid 488 through 491 No H-bonds generated for 'chain 'N' and resid 488 through 491' Processing helix chain 'N' and resid 497 through 515 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 7 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'A' and resid 192 through 195 Processing sheet with id= E, first strand: chain 'A' and resid 219 through 222 Processing sheet with id= F, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'A' and resid 476 through 479 Processing sheet with id= H, first strand: chain 'B' and resid 4 through 7 Processing sheet with id= I, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= J, first strand: chain 'B' and resid 174 through 179 Processing sheet with id= K, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= L, first strand: chain 'B' and resid 219 through 222 Processing sheet with id= M, first strand: chain 'B' and resid 411 through 413 Processing sheet with id= N, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= O, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= P, first strand: chain 'C' and resid 174 through 179 Processing sheet with id= Q, first strand: chain 'C' and resid 192 through 195 Processing sheet with id= R, first strand: chain 'C' and resid 219 through 222 Processing sheet with id= S, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= T, first strand: chain 'C' and resid 476 through 479 Processing sheet with id= U, first strand: chain 'D' and resid 4 through 7 Processing sheet with id= V, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= W, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= X, first strand: chain 'D' and resid 192 through 195 Processing sheet with id= Y, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= Z, first strand: chain 'D' and resid 411 through 413 Processing sheet with id= AA, first strand: chain 'D' and resid 476 through 479 Processing sheet with id= AB, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= AC, first strand: chain 'E' and resid 174 through 179 Processing sheet with id= AD, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= AE, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= AF, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= AG, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AH, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AI, first strand: chain 'F' and resid 174 through 179 Processing sheet with id= AJ, first strand: chain 'F' and resid 192 through 195 Processing sheet with id= AK, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= AL, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= AM, first strand: chain 'F' and resid 476 through 479 Processing sheet with id= AN, first strand: chain 'G' and resid 4 through 7 Processing sheet with id= AO, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= AP, first strand: chain 'G' and resid 174 through 179 Processing sheet with id= AQ, first strand: chain 'G' and resid 192 through 195 Processing sheet with id= AR, first strand: chain 'G' and resid 219 through 222 Processing sheet with id= AS, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= AT, first strand: chain 'G' and resid 476 through 479 Processing sheet with id= AU, first strand: chain 'H' and resid 4 through 7 Processing sheet with id= AV, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= AW, first strand: chain 'H' and resid 174 through 179 Processing sheet with id= AX, first strand: chain 'H' and resid 192 through 195 Processing sheet with id= AY, first strand: chain 'H' and resid 219 through 222 Processing sheet with id= AZ, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= BA, first strand: chain 'H' and resid 476 through 479 Processing sheet with id= BB, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= BC, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= BD, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= BE, first strand: chain 'I' and resid 192 through 195 Processing sheet with id= BF, first strand: chain 'I' and resid 219 through 222 Processing sheet with id= BG, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= BH, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= BI, first strand: chain 'J' and resid 4 through 7 Processing sheet with id= BJ, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= BK, first strand: chain 'J' and resid 174 through 179 Processing sheet with id= BL, first strand: chain 'J' and resid 192 through 195 Processing sheet with id= BM, first strand: chain 'J' and resid 219 through 222 Processing sheet with id= BN, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= BO, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= BP, first strand: chain 'K' and resid 4 through 7 Processing sheet with id= BQ, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= BR, first strand: chain 'K' and resid 174 through 179 Processing sheet with id= BS, first strand: chain 'K' and resid 192 through 195 Processing sheet with id= BT, first strand: chain 'K' and resid 219 through 222 Processing sheet with id= BU, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= BV, first strand: chain 'K' and resid 476 through 479 Processing sheet with id= BW, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= BX, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= BY, first strand: chain 'L' and resid 193 through 195 Processing sheet with id= BZ, first strand: chain 'L' and resid 219 through 222 Processing sheet with id= CA, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= CB, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= CC, first strand: chain 'M' and resid 4 through 7 Processing sheet with id= CD, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= CE, first strand: chain 'M' and resid 174 through 179 Processing sheet with id= CF, first strand: chain 'M' and resid 192 through 195 Processing sheet with id= CG, first strand: chain 'M' and resid 219 through 222 Processing sheet with id= CH, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= CI, first strand: chain 'M' and resid 476 through 479 Processing sheet with id= CJ, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= CK, first strand: chain 'N' and resid 174 through 179 Processing sheet with id= CL, first strand: chain 'N' and resid 193 through 195 Processing sheet with id= CM, first strand: chain 'N' and resid 219 through 222 Processing sheet with id= CN, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= CO, first strand: chain 'N' and resid 476 through 479 3355 hydrogen bonds defined for protein. 9690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.50 Time building geometry restraints manager: 18.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18652 1.34 - 1.46: 9056 1.46 - 1.58: 26654 1.58 - 1.70: 14 1.70 - 1.83: 518 Bond restraints: 54894 Sorted by residual: bond pdb=" CB MET C 16 " pdb=" CG MET C 16 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.40e+00 bond pdb=" SD MET L 69 " pdb=" CE MET L 69 " ideal model delta sigma weight residual 1.791 1.735 0.056 2.50e-02 1.60e+03 5.06e+00 bond pdb=" CB MET E 69 " pdb=" CG MET E 69 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.45e+00 bond pdb=" CB ASP K 41 " pdb=" CG ASP K 41 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.41e+00 bond pdb=" CB VAL F 39 " pdb=" CG1 VAL F 39 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.26e+00 ... (remaining 54889 not shown) Histogram of bond angle deviations from ideal: 95.12 - 104.01: 709 104.01 - 112.90: 31248 112.90 - 121.79: 30952 121.79 - 130.67: 11221 130.67 - 139.56: 84 Bond angle restraints: 74214 Sorted by residual: angle pdb=" CA MET M 514 " pdb=" CB MET M 514 " pdb=" CG MET M 514 " ideal model delta sigma weight residual 114.10 126.60 -12.50 2.00e+00 2.50e-01 3.91e+01 angle pdb=" CA MET E 514 " pdb=" CB MET E 514 " pdb=" CG MET E 514 " ideal model delta sigma weight residual 114.10 126.13 -12.03 2.00e+00 2.50e-01 3.62e+01 angle pdb=" CA MET A 514 " pdb=" CB MET A 514 " pdb=" CG MET A 514 " ideal model delta sigma weight residual 114.10 125.08 -10.98 2.00e+00 2.50e-01 3.01e+01 angle pdb=" N GLU B 164 " pdb=" CA GLU B 164 " pdb=" CB GLU B 164 " ideal model delta sigma weight residual 110.16 117.28 -7.12 1.48e+00 4.57e-01 2.31e+01 angle pdb=" N GLU L 164 " pdb=" CA GLU L 164 " pdb=" CB GLU L 164 " ideal model delta sigma weight residual 110.16 117.07 -6.91 1.48e+00 4.57e-01 2.18e+01 ... (remaining 74209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 30934 16.73 - 33.45: 2565 33.45 - 50.18: 609 50.18 - 66.90: 170 66.90 - 83.63: 22 Dihedral angle restraints: 34300 sinusoidal: 13566 harmonic: 20734 Sorted by residual: dihedral pdb=" CA ASP H 41 " pdb=" C ASP H 41 " pdb=" N LYS H 42 " pdb=" CA LYS H 42 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ASP I 41 " pdb=" C ASP I 41 " pdb=" N LYS I 42 " pdb=" CA LYS I 42 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASP M 41 " pdb=" C ASP M 41 " pdb=" N LYS M 42 " pdb=" CA LYS M 42 " ideal model delta harmonic sigma weight residual 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 34297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 6384 0.047 - 0.095: 1889 0.095 - 0.142: 647 0.142 - 0.190: 62 0.190 - 0.237: 20 Chirality restraints: 9002 Sorted by residual: chirality pdb=" CB VAL H 521 " pdb=" CA VAL H 521 " pdb=" CG1 VAL H 521 " pdb=" CG2 VAL H 521 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL K 521 " pdb=" CA VAL K 521 " pdb=" CG1 VAL K 521 " pdb=" CG2 VAL K 521 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB VAL G 521 " pdb=" CA VAL G 521 " pdb=" CG1 VAL G 521 " pdb=" CG2 VAL G 521 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 8999 not shown) Planarity restraints: 9632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP K 41 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" CG ASP K 41 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP K 41 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP K 41 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 41 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" CG ASP B 41 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP B 41 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 41 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 41 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" CG ASP H 41 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP H 41 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP H 41 " -0.014 2.00e-02 2.50e+03 ... (remaining 9629 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 8183 2.76 - 3.29: 56914 3.29 - 3.83: 97177 3.83 - 4.36: 111850 4.36 - 4.90: 188462 Nonbonded interactions: 462586 Sorted by model distance: nonbonded pdb=" OH TYR K 360 " pdb=" OE1 GLN L 184 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR E 360 " pdb=" OE1 GLN F 184 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR L 360 " pdb=" OE1 GLN M 184 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR H 360 " pdb=" OE1 GLN I 184 " model vdw 2.280 2.440 nonbonded pdb=" OD2 ASP E 495 " pdb=" O2' ATP E 601 " model vdw 2.299 2.440 ... (remaining 462581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.030 Extract box with map and model: 13.060 Check model and map are aligned: 0.580 Set scattering table: 0.370 Process input model: 109.930 Find NCS groups from input model: 2.970 Set up NCS constraints: 0.420 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.005 0.076 54894 Z= 0.341 Angle : 0.845 13.052 74214 Z= 0.466 Chirality : 0.051 0.237 9002 Planarity : 0.005 0.037 9632 Dihedral : 13.611 83.629 21000 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.09), residues: 7322 helix: 0.01 (0.07), residues: 4046 sheet: -0.63 (0.16), residues: 1064 loop : -0.78 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS M 401 PHE 0.025 0.002 PHE G 8 TYR 0.039 0.002 TYR D 360 ARG 0.004 0.001 ARG J 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 4.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8314 (mtp) cc_final: 0.8045 (ttm) REVERT: A 288 MET cc_start: 0.9233 (ppp) cc_final: 0.9021 (ppp) REVERT: B 16 MET cc_start: 0.8215 (ttm) cc_final: 0.7329 (ttp) REVERT: B 233 MET cc_start: 0.8534 (mmp) cc_final: 0.8308 (mmp) REVERT: C 69 MET cc_start: 0.8364 (mtt) cc_final: 0.7962 (mtt) REVERT: C 114 MET cc_start: 0.8319 (mmm) cc_final: 0.8085 (mmm) REVERT: D 233 MET cc_start: 0.8519 (mmp) cc_final: 0.8222 (mmp) REVERT: D 267 MET cc_start: 0.3479 (ttt) cc_final: 0.3268 (ttm) REVERT: E 233 MET cc_start: 0.8401 (mmp) cc_final: 0.7432 (tpp) REVERT: G 114 MET cc_start: 0.8367 (mmm) cc_final: 0.8042 (mmm) REVERT: G 233 MET cc_start: 0.8524 (mmp) cc_final: 0.8160 (mmm) REVERT: H 233 MET cc_start: 0.8656 (mmp) cc_final: 0.8401 (mmp) REVERT: I 506 TYR cc_start: 0.7620 (m-80) cc_final: 0.7398 (m-80) REVERT: J 29 VAL cc_start: 0.8987 (t) cc_final: 0.8599 (m) REVERT: J 69 MET cc_start: 0.8175 (mtp) cc_final: 0.7900 (ttm) REVERT: K 267 MET cc_start: 0.2657 (ttp) cc_final: 0.2429 (ttm) REVERT: K 520 MET cc_start: 0.8334 (mtt) cc_final: 0.8085 (mtt) REVERT: N 16 MET cc_start: 0.8375 (ttp) cc_final: 0.8090 (ttp) REVERT: N 233 MET cc_start: 0.8743 (mmp) cc_final: 0.8518 (mmm) REVERT: N 506 TYR cc_start: 0.7628 (m-80) cc_final: 0.7359 (m-80) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.4901 time to fit residues: 353.7629 Evaluate side-chains 348 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 4.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 9.9990 chunk 551 optimal weight: 50.0000 chunk 306 optimal weight: 0.1980 chunk 188 optimal weight: 30.0000 chunk 372 optimal weight: 5.9990 chunk 294 optimal weight: 4.9990 chunk 570 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 346 optimal weight: 20.0000 chunk 424 optimal weight: 7.9990 chunk 661 optimal weight: 30.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN C 37 ASN ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN J 290 GLN L 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 54894 Z= 0.341 Angle : 0.588 13.117 74214 Z= 0.317 Chirality : 0.043 0.140 9002 Planarity : 0.003 0.025 9632 Dihedral : 8.632 67.201 8218 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.64 % Allowed : 5.82 % Favored : 93.55 % 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: -0.01 (0.09), residues: 7322 helix: 0.75 (0.08), residues: 4088 sheet: -0.75 (0.16), residues: 1036 loop : -0.88 (0.11), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 401 PHE 0.020 0.002 PHE E 195 TYR 0.025 0.002 TYR A 360 ARG 0.003 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 352 time to evaluate : 4.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7602 (ttt) REVERT: A 166 MET cc_start: 0.9154 (mmm) cc_final: 0.8916 (mmm) REVERT: B 233 MET cc_start: 0.8714 (mmp) cc_final: 0.8438 (mmp) REVERT: C 16 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7461 (ttm) REVERT: D 166 MET cc_start: 0.9349 (mmm) cc_final: 0.9089 (mmm) REVERT: D 233 MET cc_start: 0.8711 (mmp) cc_final: 0.8425 (mmp) REVERT: D 520 MET cc_start: 0.8500 (mtt) cc_final: 0.8230 (mtt) REVERT: E 233 MET cc_start: 0.8479 (mmp) cc_final: 0.7709 (tpp) REVERT: E 288 MET cc_start: 0.9005 (ppp) cc_final: 0.8783 (ppp) REVERT: G 233 MET cc_start: 0.8598 (mmp) cc_final: 0.7992 (tpp) REVERT: H 233 MET cc_start: 0.8758 (mmp) cc_final: 0.8526 (mmp) REVERT: H 288 MET cc_start: 0.8977 (ppp) cc_final: 0.8694 (ppp) REVERT: I 83 ASP cc_start: 0.8327 (t0) cc_final: 0.8024 (t70) REVERT: J 288 MET cc_start: 0.8986 (ppp) cc_final: 0.8754 (ppp) REVERT: K 267 MET cc_start: 0.2743 (ttp) cc_final: 0.2462 (ttm) REVERT: L 288 MET cc_start: 0.9063 (ppp) cc_final: 0.8846 (ppp) REVERT: M 233 MET cc_start: 0.8750 (mmm) cc_final: 0.8354 (tpp) REVERT: N 233 MET cc_start: 0.8851 (mmp) cc_final: 0.8602 (mmm) outliers start: 36 outliers final: 14 residues processed: 373 average time/residue: 0.4735 time to fit residues: 310.1371 Evaluate side-chains 348 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 332 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 69 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 0.5980 chunk 205 optimal weight: 5.9990 chunk 550 optimal weight: 0.9980 chunk 450 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 662 optimal weight: 10.0000 chunk 715 optimal weight: 0.9990 chunk 589 optimal weight: 30.0000 chunk 656 optimal weight: 3.9990 chunk 225 optimal weight: 0.2980 chunk 531 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54894 Z= 0.179 Angle : 0.503 8.650 74214 Z= 0.268 Chirality : 0.040 0.140 9002 Planarity : 0.003 0.021 9632 Dihedral : 8.063 67.310 8218 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.67 % Allowed : 8.61 % Favored : 90.72 % 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: 0.35 (0.09), residues: 7322 helix: 1.21 (0.08), residues: 4144 sheet: -0.78 (0.14), residues: 1176 loop : -1.04 (0.12), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 401 PHE 0.015 0.001 PHE E 195 TYR 0.020 0.001 TYR I 360 ARG 0.002 0.000 ARG F 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 359 time to evaluate : 4.700 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: A 16 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7762 (ttt) REVERT: A 288 MET cc_start: 0.9243 (ppp) cc_final: 0.9031 (ppp) REVERT: B 233 MET cc_start: 0.8762 (mmp) cc_final: 0.8472 (mmp) REVERT: C 16 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7114 (ttm) REVERT: C 288 MET cc_start: 0.9135 (ppp) cc_final: 0.8928 (ppp) REVERT: D 233 MET cc_start: 0.8759 (mmp) cc_final: 0.8485 (mmp) REVERT: D 520 MET cc_start: 0.8360 (mtt) cc_final: 0.8124 (mtt) REVERT: E 16 MET cc_start: 0.8068 (ttt) cc_final: 0.7373 (ttt) REVERT: E 233 MET cc_start: 0.8551 (mmp) cc_final: 0.7813 (tpp) REVERT: E 288 MET cc_start: 0.9032 (ppp) cc_final: 0.8817 (ppp) REVERT: G 233 MET cc_start: 0.8671 (mmp) cc_final: 0.8037 (tpp) REVERT: G 520 MET cc_start: 0.7842 (mtt) cc_final: 0.7612 (mtt) REVERT: H 233 MET cc_start: 0.8845 (mmp) cc_final: 0.8590 (mmp) REVERT: H 288 MET cc_start: 0.9022 (ppp) cc_final: 0.8779 (ppp) REVERT: I 83 ASP cc_start: 0.8262 (t0) cc_final: 0.7945 (t70) REVERT: I 100 ILE cc_start: 0.8891 (tp) cc_final: 0.8621 (tp) REVERT: I 233 MET cc_start: 0.8779 (mmp) cc_final: 0.8567 (mmm) REVERT: J 288 MET cc_start: 0.9033 (ppp) cc_final: 0.8813 (ppp) REVERT: K 267 MET cc_start: 0.2747 (ttp) cc_final: 0.2499 (ttm) REVERT: K 520 MET cc_start: 0.8554 (mtt) cc_final: 0.8075 (mtp) REVERT: L 8 PHE cc_start: 0.7388 (p90) cc_final: 0.7016 (p90) REVERT: L 233 MET cc_start: 0.8711 (mmp) cc_final: 0.8471 (mmm) REVERT: L 288 MET cc_start: 0.9090 (ppp) cc_final: 0.8886 (ppp) REVERT: M 41 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: M 288 MET cc_start: 0.9191 (ppp) cc_final: 0.8931 (ppp) REVERT: N 114 MET cc_start: 0.8563 (mmm) cc_final: 0.8282 (mmm) outliers start: 38 outliers final: 16 residues processed: 381 average time/residue: 0.4966 time to fit residues: 330.3651 Evaluate side-chains 356 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 337 time to evaluate : 4.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 164 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 0.5980 chunk 497 optimal weight: 20.0000 chunk 343 optimal weight: 50.0000 chunk 73 optimal weight: 9.9990 chunk 316 optimal weight: 0.9990 chunk 444 optimal weight: 10.0000 chunk 664 optimal weight: 10.0000 chunk 703 optimal weight: 8.9990 chunk 347 optimal weight: 8.9990 chunk 629 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 GLN ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 54894 Z= 0.386 Angle : 0.594 12.046 74214 Z= 0.316 Chirality : 0.043 0.136 9002 Planarity : 0.003 0.025 9632 Dihedral : 8.001 67.247 8218 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.31 % Allowed : 10.04 % Favored : 88.65 % 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: 0.34 (0.09), residues: 7322 helix: 1.11 (0.08), residues: 4158 sheet: -0.75 (0.14), residues: 1148 loop : -0.86 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 401 PHE 0.018 0.002 PHE F 8 TYR 0.019 0.002 TYR I 360 ARG 0.004 0.000 ARG G 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 329 time to evaluate : 4.724 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: A 16 MET cc_start: 0.8174 (ttt) cc_final: 0.7904 (ttt) REVERT: A 520 MET cc_start: 0.8092 (mtm) cc_final: 0.7875 (mtp) REVERT: B 164 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.9004 (mt-10) REVERT: B 233 MET cc_start: 0.8959 (mmp) cc_final: 0.8617 (mmp) REVERT: C 164 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8816 (mt-10) REVERT: D 233 MET cc_start: 0.8797 (mmp) cc_final: 0.8194 (tpp) REVERT: E 69 MET cc_start: 0.8452 (mmm) cc_final: 0.8242 (mtt) REVERT: E 233 MET cc_start: 0.8669 (mmp) cc_final: 0.7992 (tpp) REVERT: E 288 MET cc_start: 0.9046 (ppp) cc_final: 0.8820 (ppp) REVERT: F 41 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: F 233 MET cc_start: 0.8313 (mmm) cc_final: 0.8060 (mmp) REVERT: G 233 MET cc_start: 0.8710 (mmp) cc_final: 0.8215 (tpp) REVERT: H 233 MET cc_start: 0.8916 (mmp) cc_final: 0.8668 (mmp) REVERT: H 288 MET cc_start: 0.9025 (ppp) cc_final: 0.8773 (ppp) REVERT: I 233 MET cc_start: 0.8809 (mmp) cc_final: 0.8538 (mmp) REVERT: J 233 MET cc_start: 0.8731 (mmp) cc_final: 0.8482 (mmp) REVERT: K 520 MET cc_start: 0.8461 (mtt) cc_final: 0.8202 (mtt) REVERT: M 41 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7380 (m-30) outliers start: 74 outliers final: 45 residues processed: 392 average time/residue: 0.4881 time to fit residues: 333.9473 Evaluate side-chains 371 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 322 time to evaluate : 4.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 6 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 521 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 0.9980 chunk 399 optimal weight: 50.0000 chunk 10 optimal weight: 0.9980 chunk 523 optimal weight: 0.6980 chunk 290 optimal weight: 2.9990 chunk 600 optimal weight: 7.9990 chunk 486 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 631 optimal weight: 0.7980 chunk 177 optimal weight: 10.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54894 Z= 0.180 Angle : 0.507 8.850 74214 Z= 0.268 Chirality : 0.040 0.139 9002 Planarity : 0.003 0.021 9632 Dihedral : 7.527 67.275 8218 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.11 % Allowed : 11.10 % Favored : 87.78 % 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: 0.58 (0.10), residues: 7322 helix: 1.36 (0.08), residues: 4158 sheet: -0.88 (0.14), residues: 1176 loop : -0.73 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS N 401 PHE 0.011 0.001 PHE F 8 TYR 0.017 0.001 TYR C 360 ARG 0.002 0.000 ARG K 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 354 time to evaluate : 4.794 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: B 233 MET cc_start: 0.8968 (mmp) cc_final: 0.8636 (mmp) REVERT: B 288 MET cc_start: 0.9106 (ppp) cc_final: 0.8884 (ppp) REVERT: C 164 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8889 (mt-10) REVERT: C 233 MET cc_start: 0.8650 (mmm) cc_final: 0.8442 (mmp) REVERT: D 164 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8835 (mt-10) REVERT: D 166 MET cc_start: 0.9298 (mmm) cc_final: 0.9055 (mmm) REVERT: D 233 MET cc_start: 0.8824 (mmp) cc_final: 0.8332 (tpp) REVERT: E 69 MET cc_start: 0.8535 (mmm) cc_final: 0.8222 (mtt) REVERT: E 233 MET cc_start: 0.8669 (mmp) cc_final: 0.7994 (tpp) REVERT: E 288 MET cc_start: 0.9057 (ppp) cc_final: 0.8834 (ppp) REVERT: F 41 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7244 (m-30) REVERT: G 16 MET cc_start: 0.8169 (ttm) cc_final: 0.7610 (ttm) REVERT: G 233 MET cc_start: 0.8732 (mmp) cc_final: 0.8216 (tpp) REVERT: G 288 MET cc_start: 0.9194 (ppp) cc_final: 0.8978 (ppp) REVERT: H 41 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: H 288 MET cc_start: 0.9050 (ppp) cc_final: 0.8781 (ppp) REVERT: I 83 ASP cc_start: 0.8287 (t0) cc_final: 0.7973 (t70) REVERT: I 233 MET cc_start: 0.8742 (mmp) cc_final: 0.8540 (mmp) REVERT: J 114 MET cc_start: 0.8340 (mmm) cc_final: 0.8091 (mmm) REVERT: J 233 MET cc_start: 0.8717 (mmp) cc_final: 0.8487 (mmp) REVERT: J 288 MET cc_start: 0.9067 (ppp) cc_final: 0.8786 (ppp) REVERT: K 233 MET cc_start: 0.8705 (mmp) cc_final: 0.8487 (mmp) REVERT: M 16 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7970 (ttt) REVERT: M 41 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: N 69 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7948 (mtt) REVERT: N 233 MET cc_start: 0.8913 (mmp) cc_final: 0.8703 (mmm) REVERT: N 288 MET cc_start: 0.9170 (ppp) cc_final: 0.8925 (ppp) outliers start: 63 outliers final: 33 residues processed: 399 average time/residue: 0.4817 time to fit residues: 338.2364 Evaluate side-chains 374 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 334 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 363 GLU Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 16 MET Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 69 MET Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 521 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 5.9990 chunk 633 optimal weight: 0.7980 chunk 139 optimal weight: 30.0000 chunk 413 optimal weight: 4.9990 chunk 173 optimal weight: 30.0000 chunk 704 optimal weight: 6.9990 chunk 584 optimal weight: 4.9990 chunk 326 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 232 optimal weight: 30.0000 chunk 369 optimal weight: 0.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 54894 Z= 0.250 Angle : 0.530 9.457 74214 Z= 0.280 Chirality : 0.041 0.139 9002 Planarity : 0.003 0.021 9632 Dihedral : 7.231 66.316 8218 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.40 % Allowed : 12.02 % Favored : 86.58 % 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: 0.64 (0.10), residues: 7322 helix: 1.35 (0.08), residues: 4200 sheet: -0.89 (0.14), residues: 1176 loop : -0.58 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.030 0.001 PHE C 195 TYR 0.020 0.001 TYR C 360 ARG 0.002 0.000 ARG K 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 349 time to evaluate : 4.691 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: A 69 MET cc_start: 0.8560 (mtp) cc_final: 0.8314 (ttm) REVERT: A 288 MET cc_start: 0.9123 (ppp) cc_final: 0.8760 (ppp) REVERT: B 233 MET cc_start: 0.9011 (mmp) cc_final: 0.8668 (mmp) REVERT: C 288 MET cc_start: 0.9152 (ppp) cc_final: 0.8929 (ppp) REVERT: D 166 MET cc_start: 0.9290 (mmm) cc_final: 0.8980 (mmm) REVERT: D 233 MET cc_start: 0.8883 (mmp) cc_final: 0.8571 (mmp) REVERT: E 69 MET cc_start: 0.8519 (mmm) cc_final: 0.8215 (mtt) REVERT: E 233 MET cc_start: 0.8735 (mmp) cc_final: 0.8102 (tpp) REVERT: E 288 MET cc_start: 0.9077 (ppp) cc_final: 0.8840 (ppp) REVERT: F 41 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: F 69 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8266 (ttm) REVERT: G 233 MET cc_start: 0.8762 (mmp) cc_final: 0.8298 (tpp) REVERT: H 41 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8061 (t0) REVERT: H 288 MET cc_start: 0.9064 (ppp) cc_final: 0.8796 (ppp) REVERT: I 83 ASP cc_start: 0.8264 (t0) cc_final: 0.7994 (t70) REVERT: I 233 MET cc_start: 0.8735 (mmp) cc_final: 0.8519 (mmp) REVERT: J 233 MET cc_start: 0.8743 (mmp) cc_final: 0.8472 (mmp) REVERT: J 288 MET cc_start: 0.9019 (ppp) cc_final: 0.8744 (ppp) REVERT: J 307 MET cc_start: 0.7730 (pmm) cc_final: 0.7525 (pmm) REVERT: L 233 MET cc_start: 0.8732 (mmp) cc_final: 0.7916 (tpp) REVERT: L 288 MET cc_start: 0.9112 (ppp) cc_final: 0.8844 (ppp) REVERT: M 41 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: M 233 MET cc_start: 0.8744 (mmm) cc_final: 0.8521 (mmp) REVERT: M 288 MET cc_start: 0.9150 (ppp) cc_final: 0.8868 (ppp) REVERT: N 111 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8018 (mtt) REVERT: N 233 MET cc_start: 0.8865 (mmp) cc_final: 0.8637 (mmm) outliers start: 79 outliers final: 54 residues processed: 407 average time/residue: 0.4773 time to fit residues: 341.4257 Evaluate side-chains 396 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 337 time to evaluate : 4.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 363 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 363 GLU Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 521 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 401 optimal weight: 9.9990 chunk 514 optimal weight: 0.0980 chunk 398 optimal weight: 9.9990 chunk 592 optimal weight: 0.9990 chunk 393 optimal weight: 8.9990 chunk 701 optimal weight: 50.0000 chunk 439 optimal weight: 10.0000 chunk 427 optimal weight: 2.9990 chunk 323 optimal weight: 3.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 54894 Z= 0.216 Angle : 0.524 9.815 74214 Z= 0.275 Chirality : 0.041 0.138 9002 Planarity : 0.003 0.021 9632 Dihedral : 7.016 67.038 8218 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.59 % Allowed : 12.29 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.10), residues: 7322 helix: 1.43 (0.08), residues: 4172 sheet: -0.48 (0.14), residues: 1190 loop : -0.69 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.022 0.001 PHE C 195 TYR 0.013 0.001 TYR F 360 ARG 0.002 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 354 time to evaluate : 4.766 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: A 69 MET cc_start: 0.8452 (mtp) cc_final: 0.8179 (ttm) REVERT: A 233 MET cc_start: 0.8673 (mmm) cc_final: 0.8249 (mmp) REVERT: B 233 MET cc_start: 0.9033 (mmp) cc_final: 0.8714 (mmp) REVERT: C 288 MET cc_start: 0.9171 (ppp) cc_final: 0.8963 (ppp) REVERT: D 233 MET cc_start: 0.8914 (mmp) cc_final: 0.8596 (mmp) REVERT: D 288 MET cc_start: 0.9172 (ppp) cc_final: 0.8925 (ppp) REVERT: E 69 MET cc_start: 0.8489 (mmm) cc_final: 0.8194 (mtt) REVERT: E 233 MET cc_start: 0.8732 (mmp) cc_final: 0.8113 (tpp) REVERT: E 288 MET cc_start: 0.9091 (ppp) cc_final: 0.8844 (ppp) REVERT: F 41 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: F 69 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8248 (ttm) REVERT: F 288 MET cc_start: 0.9057 (ppp) cc_final: 0.8816 (ppp) REVERT: G 233 MET cc_start: 0.8738 (mmp) cc_final: 0.8294 (tpp) REVERT: G 288 MET cc_start: 0.9189 (ppp) cc_final: 0.8826 (ppp) REVERT: H 41 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8008 (m-30) REVERT: H 288 MET cc_start: 0.9053 (ppp) cc_final: 0.8781 (ppp) REVERT: I 83 ASP cc_start: 0.8264 (t0) cc_final: 0.7988 (t70) REVERT: I 233 MET cc_start: 0.8734 (mmp) cc_final: 0.8521 (mmp) REVERT: J 69 MET cc_start: 0.8704 (ttt) cc_final: 0.8502 (ttm) REVERT: J 233 MET cc_start: 0.8744 (mmp) cc_final: 0.8462 (mmp) REVERT: J 288 MET cc_start: 0.9054 (ppp) cc_final: 0.8792 (ppp) REVERT: M 41 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: M 233 MET cc_start: 0.8792 (mmm) cc_final: 0.8575 (mmp) REVERT: N 111 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.7991 (mtt) REVERT: N 233 MET cc_start: 0.8857 (mmp) cc_final: 0.8620 (mmm) REVERT: N 288 MET cc_start: 0.9179 (ppp) cc_final: 0.8812 (ppp) outliers start: 90 outliers final: 63 residues processed: 425 average time/residue: 0.4739 time to fit residues: 354.8653 Evaluate side-chains 409 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 341 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 363 GLU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 363 GLU Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain M residue 6 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 50 THR Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 0.0570 chunk 280 optimal weight: 7.9990 chunk 419 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 135 optimal weight: 40.0000 chunk 446 optimal weight: 0.8980 chunk 478 optimal weight: 2.9990 chunk 346 optimal weight: 6.9990 chunk 65 optimal weight: 0.0040 chunk 551 optimal weight: 50.0000 overall best weight: 0.5912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 54894 Z= 0.144 Angle : 0.513 13.088 74214 Z= 0.266 Chirality : 0.040 0.142 9002 Planarity : 0.003 0.024 9632 Dihedral : 6.617 68.147 8218 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.18 % Allowed : 13.22 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.10), residues: 7322 helix: 1.71 (0.08), residues: 4102 sheet: -0.70 (0.14), residues: 1176 loop : -0.58 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS N 401 PHE 0.034 0.001 PHE E 195 TYR 0.016 0.001 TYR F 360 ARG 0.003 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 384 time to evaluate : 4.656 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: A 233 MET cc_start: 0.8726 (mmm) cc_final: 0.8332 (mmp) REVERT: B 233 MET cc_start: 0.9024 (mmp) cc_final: 0.8706 (mmp) REVERT: C 288 MET cc_start: 0.9184 (ppp) cc_final: 0.8955 (ppp) REVERT: D 233 MET cc_start: 0.8961 (mmp) cc_final: 0.8615 (mmp) REVERT: D 288 MET cc_start: 0.9195 (ppp) cc_final: 0.8935 (ppp) REVERT: E 69 MET cc_start: 0.8437 (mmm) cc_final: 0.8136 (mtt) REVERT: E 100 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8050 (tt) REVERT: E 233 MET cc_start: 0.8734 (mmp) cc_final: 0.8114 (tpp) REVERT: F 41 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: F 69 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8058 (ttm) REVERT: G 233 MET cc_start: 0.8740 (mmp) cc_final: 0.8271 (tpp) REVERT: G 288 MET cc_start: 0.9180 (ppp) cc_final: 0.8822 (ppp) REVERT: H 41 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: H 288 MET cc_start: 0.9053 (ppp) cc_final: 0.8774 (ppp) REVERT: I 114 MET cc_start: 0.8464 (mmm) cc_final: 0.8026 (mmm) REVERT: I 166 MET cc_start: 0.9180 (mmm) cc_final: 0.8971 (mmm) REVERT: I 233 MET cc_start: 0.8728 (mmp) cc_final: 0.8508 (mmp) REVERT: J 114 MET cc_start: 0.8323 (mmm) cc_final: 0.8067 (mmm) REVERT: J 307 MET cc_start: 0.7620 (pmm) cc_final: 0.7347 (pmm) REVERT: K 520 MET cc_start: 0.8018 (mtt) cc_final: 0.7640 (mtt) REVERT: L 69 MET cc_start: 0.8465 (mtt) cc_final: 0.8142 (mmm) REVERT: L 233 MET cc_start: 0.8656 (mmm) cc_final: 0.8449 (mmp) REVERT: L 288 MET cc_start: 0.9132 (ppp) cc_final: 0.8837 (ppp) REVERT: M 41 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: M 69 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8107 (mtt) REVERT: M 114 MET cc_start: 0.8243 (mmm) cc_final: 0.7933 (mmm) REVERT: M 233 MET cc_start: 0.8833 (mmm) cc_final: 0.8627 (mmp) REVERT: M 288 MET cc_start: 0.9131 (ppp) cc_final: 0.8878 (ppp) REVERT: N 111 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7882 (mtt) REVERT: N 114 MET cc_start: 0.8577 (mmm) cc_final: 0.8248 (mmm) REVERT: N 233 MET cc_start: 0.8871 (mmp) cc_final: 0.8638 (mmm) REVERT: N 288 MET cc_start: 0.9168 (ppp) cc_final: 0.8800 (ppp) REVERT: N 506 TYR cc_start: 0.7710 (m-80) cc_final: 0.7277 (m-80) outliers start: 67 outliers final: 47 residues processed: 443 average time/residue: 0.5056 time to fit residues: 394.4116 Evaluate side-chains 405 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 351 time to evaluate : 4.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 363 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 363 GLU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 7.9990 chunk 672 optimal weight: 5.9990 chunk 613 optimal weight: 5.9990 chunk 653 optimal weight: 30.0000 chunk 393 optimal weight: 30.0000 chunk 284 optimal weight: 3.9990 chunk 513 optimal weight: 0.2980 chunk 200 optimal weight: 0.9990 chunk 590 optimal weight: 9.9990 chunk 618 optimal weight: 0.7980 chunk 651 optimal weight: 40.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 54894 Z= 0.245 Angle : 0.561 12.466 74214 Z= 0.291 Chirality : 0.041 0.156 9002 Planarity : 0.003 0.023 9632 Dihedral : 6.597 66.234 8218 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.26 % Allowed : 13.83 % Favored : 84.92 % 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: 0.92 (0.10), residues: 7322 helix: 1.61 (0.08), residues: 4144 sheet: -0.70 (0.14), residues: 1176 loop : -0.55 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.034 0.002 PHE C 195 TYR 0.016 0.001 TYR F 360 ARG 0.002 0.000 ARG M 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 353 time to evaluate : 4.640 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: A 233 MET cc_start: 0.8858 (mmm) cc_final: 0.8489 (mmp) REVERT: B 233 MET cc_start: 0.9037 (mmp) cc_final: 0.8720 (mmp) REVERT: B 288 MET cc_start: 0.9101 (ppp) cc_final: 0.8860 (ppp) REVERT: D 233 MET cc_start: 0.9004 (mmp) cc_final: 0.8641 (mmp) REVERT: D 288 MET cc_start: 0.9189 (ppp) cc_final: 0.8929 (ppp) REVERT: E 69 MET cc_start: 0.8456 (mmm) cc_final: 0.8182 (mtt) REVERT: E 233 MET cc_start: 0.8756 (mmp) cc_final: 0.8161 (tpp) REVERT: E 288 MET cc_start: 0.9041 (ppp) cc_final: 0.8801 (ppp) REVERT: F 41 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: G 69 MET cc_start: 0.8642 (mtt) cc_final: 0.7946 (mtt) REVERT: G 233 MET cc_start: 0.8761 (mmp) cc_final: 0.8343 (tpp) REVERT: H 41 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7649 (t0) REVERT: H 288 MET cc_start: 0.9061 (ppp) cc_final: 0.8784 (ppp) REVERT: I 233 MET cc_start: 0.8785 (mmp) cc_final: 0.8552 (mmp) REVERT: I 389 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6561 (mmt) REVERT: J 307 MET cc_start: 0.7691 (pmm) cc_final: 0.7489 (pmm) REVERT: L 288 MET cc_start: 0.9113 (ppp) cc_final: 0.8836 (ppp) REVERT: M 41 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: M 233 MET cc_start: 0.8860 (mmm) cc_final: 0.8640 (mmp) REVERT: N 69 MET cc_start: 0.8638 (mtp) cc_final: 0.8370 (mmm) REVERT: N 111 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7919 (mtt) REVERT: N 233 MET cc_start: 0.8816 (mmp) cc_final: 0.8590 (mmm) REVERT: N 288 MET cc_start: 0.9172 (ppp) cc_final: 0.8941 (ppp) outliers start: 71 outliers final: 50 residues processed: 413 average time/residue: 0.4719 time to fit residues: 343.4075 Evaluate side-chains 400 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 345 time to evaluate : 4.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 363 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 363 GLU Chi-restraints excluded: chain J residue 514 MET Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 6.9990 chunk 691 optimal weight: 0.9990 chunk 422 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 480 optimal weight: 4.9990 chunk 725 optimal weight: 9.9990 chunk 667 optimal weight: 6.9990 chunk 577 optimal weight: 0.0970 chunk 59 optimal weight: 0.9980 chunk 446 optimal weight: 4.9990 chunk 354 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 54894 Z= 0.219 Angle : 0.563 13.523 74214 Z= 0.290 Chirality : 0.041 0.152 9002 Planarity : 0.003 0.023 9632 Dihedral : 6.555 67.411 8218 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.11 % Allowed : 14.07 % Favored : 84.81 % 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: 0.91 (0.10), residues: 7322 helix: 1.58 (0.08), residues: 4144 sheet: -0.66 (0.14), residues: 1176 loop : -0.52 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.030 0.002 PHE C 195 TYR 0.017 0.001 TYR F 360 ARG 0.002 0.000 ARG A 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 354 time to evaluate : 4.630 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: A 233 MET cc_start: 0.8845 (mmm) cc_final: 0.8475 (mmp) REVERT: B 233 MET cc_start: 0.9041 (mmp) cc_final: 0.8725 (mmp) REVERT: B 288 MET cc_start: 0.9147 (ppp) cc_final: 0.8906 (ppp) REVERT: D 233 MET cc_start: 0.9021 (mmp) cc_final: 0.8666 (mmp) REVERT: D 288 MET cc_start: 0.9184 (ppp) cc_final: 0.8923 (ppp) REVERT: E 69 MET cc_start: 0.8428 (mmm) cc_final: 0.8172 (mtt) REVERT: E 233 MET cc_start: 0.8815 (mmp) cc_final: 0.8219 (tpp) REVERT: E 288 MET cc_start: 0.9051 (ppp) cc_final: 0.8841 (ppp) REVERT: F 41 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7219 (m-30) REVERT: F 114 MET cc_start: 0.8288 (mmm) cc_final: 0.7986 (mmm) REVERT: F 288 MET cc_start: 0.9025 (ppp) cc_final: 0.8812 (ppp) REVERT: G 69 MET cc_start: 0.8495 (mtt) cc_final: 0.8131 (mtt) REVERT: G 233 MET cc_start: 0.8786 (mmp) cc_final: 0.8367 (tpp) REVERT: H 16 MET cc_start: 0.8412 (ttm) cc_final: 0.8202 (ttm) REVERT: H 41 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7606 (t0) REVERT: H 69 MET cc_start: 0.8421 (mtp) cc_final: 0.8166 (ttt) REVERT: H 73 MET cc_start: 0.7895 (mtp) cc_final: 0.7244 (mtp) REVERT: H 288 MET cc_start: 0.9062 (ppp) cc_final: 0.8783 (ppp) REVERT: I 114 MET cc_start: 0.8475 (mmm) cc_final: 0.8041 (mmm) REVERT: I 233 MET cc_start: 0.8756 (mmp) cc_final: 0.8537 (mmp) REVERT: I 288 MET cc_start: 0.9278 (ppp) cc_final: 0.9010 (ppp) REVERT: I 389 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6649 (mmt) REVERT: J 307 MET cc_start: 0.7702 (pmm) cc_final: 0.7432 (pmm) REVERT: L 288 MET cc_start: 0.9125 (ppp) cc_final: 0.8857 (ppp) REVERT: M 41 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: M 69 MET cc_start: 0.8226 (ttp) cc_final: 0.7864 (ttm) REVERT: M 233 MET cc_start: 0.8841 (mmm) cc_final: 0.8624 (mmp) REVERT: N 111 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7962 (mtt) REVERT: N 114 MET cc_start: 0.8605 (mmm) cc_final: 0.8282 (mmm) REVERT: N 233 MET cc_start: 0.8825 (mmp) cc_final: 0.8594 (mmm) outliers start: 63 outliers final: 53 residues processed: 410 average time/residue: 0.4779 time to fit residues: 345.8088 Evaluate side-chains 407 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 349 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 363 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 517 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 363 GLU Chi-restraints excluded: chain J residue 514 MET Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 2.9990 chunk 615 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 532 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 578 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 593 optimal weight: 50.0000 chunk 73 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.107302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.075237 restraints weight = 165300.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072850 restraints weight = 117604.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073581 restraints weight = 93488.108| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 54894 Z= 0.271 Angle : 0.585 13.723 74214 Z= 0.302 Chirality : 0.042 0.161 9002 Planarity : 0.003 0.022 9632 Dihedral : 6.586 66.916 8218 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.29 % Allowed : 14.02 % Favored : 84.69 % 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: 0.85 (0.10), residues: 7322 helix: 1.51 (0.08), residues: 4144 sheet: -0.69 (0.14), residues: 1176 loop : -0.51 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.028 0.002 PHE C 195 TYR 0.017 0.001 TYR F 360 ARG 0.003 0.000 ARG J 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7405.58 seconds wall clock time: 134 minutes 44.36 seconds (8084.36 seconds total)