Starting phenix.real_space_refine on Mon Mar 11 01:25:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl7_16102/03_2024/8bl7_16102_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl7_16102/03_2024/8bl7_16102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl7_16102/03_2024/8bl7_16102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl7_16102/03_2024/8bl7_16102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl7_16102/03_2024/8bl7_16102_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl7_16102/03_2024/8bl7_16102_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 ASP 5": "OD1" <-> "OD2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 461": "OE1" <-> "OE2" 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 GLU 61": "OE1" <-> "OE2" Residue "B ASP 64": "OD1" <-> "OD2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 495": "OD1" <-> "OD2" Residue "B TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C ASP 473": "OD1" <-> "OD2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 495": "OD1" <-> "OD2" Residue "C TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "D ASP 473": "OD1" <-> "OD2" 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 TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 461": "OE1" <-> "OE2" Residue "E ASP 473": "OD1" <-> "OD2" Residue "E TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 5": "OD1" <-> "OD2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 461": "OE1" <-> "OE2" Residue "F ASP 473": "OD1" <-> "OD2" Residue "F TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 64": "OD1" <-> "OD2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 495": "OD1" <-> "OD2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H ASP 83": "OD1" <-> "OD2" Residue "H TYR 199": "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 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 66": "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 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 461": "OE1" <-> "OE2" Residue "J TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 495": "OD1" <-> "OD2" Residue "K ASP 5": "OD1" <-> "OD2" Residue "K PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 63": "OE1" <-> "OE2" Residue "K GLU 67": "OE1" <-> "OE2" Residue "K TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 359": "OD1" <-> "OD2" Residue "K GLU 461": "OE1" <-> "OE2" Residue "K ASP 473": "OD1" <-> "OD2" 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 GLU 61": "OE1" <-> "OE2" Residue "L ASP 64": "OD1" <-> "OD2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 461": "OE1" <-> "OE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 495": "OD1" <-> "OD2" Residue "L TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 5": "OD1" <-> "OD2" Residue "M PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 461": "OE1" <-> "OE2" Residue "M ASP 473": "OD1" <-> "OD2" Residue "M TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 5": "OD1" <-> "OD2" Residue "N PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 63": "OE1" <-> "OE2" Residue "N ASP 64": "OD1" <-> "OD2" Residue "N ASP 83": "OD1" <-> "OD2" Residue "N TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 428": "OD1" <-> "OD2" Residue "N TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 495": "OD1" <-> "OD2" Residue "N TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s 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: 21.11, per 1000 atoms: 0.39 Number of scatterers: 54474 At special positions: 0 Unit cell: (153.6, 154.56, 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: 15.73 Conformation dependent library (CDL) restraints added in 8.5 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: 278 helices and 96 sheets defined 53.4% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.56 Creating SS restraints... Processing helix chain 'A' and resid 10 through 30 removed outlier: 4.827A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.822A pdb=" N GLU A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 84 Processing helix chain 'A' and resid 89 through 108 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 169 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 426 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: 4.920A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.692A pdb=" N GLU B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 85 Processing helix chain 'B' and resid 89 through 108 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 169 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 355 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 426 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: 4.935A 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 133 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 156 through 169 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 355 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 426 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 28 Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 65 through 84 Processing helix chain 'D' and resid 89 through 109 Processing helix chain 'D' and resid 113 through 133 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 355 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 426 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: 4.944A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 removed outlier: 3.568A pdb=" N GLU E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 84 Processing helix chain 'E' and resid 89 through 108 Processing helix chain 'E' and resid 113 through 133 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 426 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: 4.848A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 removed outlier: 3.715A pdb=" N GLU F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 84 Processing helix chain 'F' and resid 89 through 109 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 355 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 426 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: 4.907A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 65 through 84 Processing helix chain 'G' and resid 89 through 108 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 169 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 355 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 425 Processing helix chain 'G' and resid 434 through 446 Processing helix chain 'G' and resid 449 through 458 Processing helix chain 'G' and resid 462 through 471 Processing helix chain 'G' and resid 497 through 515 Processing helix chain 'H' and resid 10 through 30 removed outlier: 4.865A 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 84 Processing helix chain 'H' and resid 89 through 109 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 355 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 426 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: 4.979A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 65 through 84 Processing helix chain 'I' and resid 89 through 109 removed outlier: 3.518A pdb=" N ALA I 109 " --> pdb=" O LYS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 133 Processing helix chain 'I' and resid 141 through 151 Processing helix chain 'I' and resid 156 through 169 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 426 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 28 Processing helix chain 'J' and resid 53 through 59 removed outlier: 3.612A pdb=" N GLU J 59 " --> pdb=" O SER J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 84 Processing helix chain 'J' and resid 89 through 108 Processing helix chain 'J' and resid 113 through 133 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 355 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 426 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: 4.916A 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 84 Processing helix chain 'K' and resid 89 through 109 Processing helix chain 'K' and resid 113 through 133 Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 156 through 169 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 355 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 426 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: 5.000A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 removed outlier: 3.696A pdb=" N GLU L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 84 Processing helix chain 'L' and resid 89 through 109 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 426 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: 4.832A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 removed outlier: 3.801A pdb=" N GLU M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 84 Processing helix chain 'M' and resid 89 through 109 Processing helix chain 'M' and resid 113 through 133 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 426 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: 4.908A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 57 Processing helix chain 'N' and resid 65 through 84 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 169 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 355 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 426 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 497 through 515 Processing sheet with id= A, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= C, first strand: chain 'A' and resid 192 through 195 Processing sheet with id= D, first strand: chain 'A' and resid 219 through 222 Processing sheet with id= E, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= F, first strand: chain 'A' and resid 476 through 479 Processing sheet with id= G, first strand: chain 'B' and resid 4 through 7 Processing sheet with id= H, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= I, first strand: chain 'B' and resid 174 through 179 Processing sheet with id= J, first strand: chain 'B' and resid 192 through 195 Processing sheet with id= K, first strand: chain 'B' and resid 219 through 222 removed outlier: 6.073A pdb=" N LYS B 272 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE B 249 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 274 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA B 251 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL B 276 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 411 through 413 Processing sheet with id= M, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= N, first strand: chain 'C' and resid 4 through 7 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 removed outlier: 6.061A pdb=" N LYS C 272 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE C 249 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA C 274 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ALA C 251 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL C 276 " --> pdb=" O ALA C 251 " (cutoff:3.500A) 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 175 through 179 removed outlier: 6.426A pdb=" N ALA D 377 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLU D 178 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE D 379 " --> pdb=" O GLU D 178 " (cutoff:3.500A) 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 4 through 7 removed outlier: 3.514A pdb=" N LYS E 7 " --> pdb=" O MET E 520 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= AD, first strand: chain 'E' and resid 174 through 179 Processing sheet with id= AE, first strand: chain 'E' and resid 192 through 195 Processing sheet with id= AF, first strand: chain 'E' and resid 219 through 222 removed outlier: 6.110A pdb=" N LYS E 272 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE E 249 " --> pdb=" O LYS E 272 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA E 274 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ALA E 251 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL E 276 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= AH, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AI, first strand: chain 'F' and resid 4 through 7 Processing sheet with id= AJ, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AK, first strand: chain 'F' and resid 174 through 179 Processing sheet with id= AL, first strand: chain 'F' and resid 192 through 195 Processing sheet with id= AM, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= AN, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= AO, first strand: chain 'F' and resid 476 through 479 Processing sheet with id= AP, first strand: chain 'G' and resid 4 through 7 Processing sheet with id= AQ, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= AR, first strand: chain 'G' and resid 175 through 179 removed outlier: 6.566A pdb=" N ALA G 377 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLU G 178 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE G 379 " --> pdb=" O GLU G 178 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'G' and resid 192 through 195 Processing sheet with id= AT, first strand: chain 'G' and resid 219 through 222 removed outlier: 6.180A pdb=" N LYS G 272 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE G 249 " --> pdb=" O LYS G 272 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA G 274 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA G 251 " --> pdb=" O ALA G 274 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL G 276 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= AV, first strand: chain 'G' and resid 476 through 479 Processing sheet with id= AW, first strand: chain 'H' and resid 4 through 7 Processing sheet with id= AX, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= AY, first strand: chain 'H' and resid 174 through 179 Processing sheet with id= AZ, first strand: chain 'H' and resid 192 through 195 Processing sheet with id= BA, first strand: chain 'H' and resid 219 through 222 Processing sheet with id= BB, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= BC, first strand: chain 'H' and resid 476 through 479 Processing sheet with id= BD, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= BE, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= BF, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= BG, first strand: chain 'I' and resid 192 through 195 Processing sheet with id= BH, first strand: chain 'I' and resid 219 through 222 removed outlier: 6.051A pdb=" N LYS I 272 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE I 249 " --> pdb=" O LYS I 272 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA I 274 " --> pdb=" O ILE I 249 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA I 251 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL I 276 " --> pdb=" O ALA I 251 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= BJ, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= BK, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= BL, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= BM, first strand: chain 'J' and resid 174 through 179 Processing sheet with id= BN, first strand: chain 'J' and resid 192 through 195 Processing sheet with id= BO, first strand: chain 'J' and resid 219 through 222 removed outlier: 6.088A pdb=" N LYS J 272 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE J 249 " --> pdb=" O LYS J 272 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA J 274 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ALA J 251 " --> pdb=" O ALA J 274 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL J 276 " --> pdb=" O ALA J 251 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= BQ, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= BR, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= BS, first strand: chain 'K' and resid 174 through 179 Processing sheet with id= BT, first strand: chain 'K' and resid 192 through 195 Processing sheet with id= BU, first strand: chain 'K' and resid 219 through 222 removed outlier: 6.089A pdb=" N LYS K 272 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE K 249 " --> pdb=" O LYS K 272 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA K 274 " --> pdb=" O ILE K 249 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA K 251 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL K 276 " --> pdb=" O ALA K 251 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= BW, first strand: chain 'K' and resid 476 through 479 Processing sheet with id= BX, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= BY, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= BZ, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= CA, first strand: chain 'L' and resid 192 through 195 Processing sheet with id= CB, first strand: chain 'L' and resid 219 through 222 removed outlier: 6.177A pdb=" N LYS L 272 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE L 249 " --> pdb=" O LYS L 272 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA L 274 " --> pdb=" O ILE L 249 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA L 251 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL L 276 " --> pdb=" O ALA L 251 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= CD, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= CE, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.530A pdb=" N LYS M 7 " --> pdb=" O MET M 520 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= CG, first strand: chain 'M' and resid 174 through 179 Processing sheet with id= CH, first strand: chain 'M' and resid 192 through 195 Processing sheet with id= CI, first strand: chain 'M' and resid 219 through 222 removed outlier: 6.140A pdb=" N LYS M 272 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE M 249 " --> pdb=" O LYS M 272 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA M 274 " --> pdb=" O ILE M 249 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA M 251 " --> pdb=" O ALA M 274 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL M 276 " --> pdb=" O ALA M 251 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= CK, first strand: chain 'M' and resid 476 through 479 Processing sheet with id= CL, first strand: chain 'N' and resid 4 through 7 Processing sheet with id= CM, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= CN, first strand: chain 'N' and resid 175 through 179 removed outlier: 6.333A pdb=" N ALA N 377 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLU N 178 " --> pdb=" O ALA N 377 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE N 379 " --> pdb=" O GLU N 178 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'N' and resid 192 through 195 Processing sheet with id= CP, first strand: chain 'N' and resid 219 through 222 removed outlier: 6.175A pdb=" N LYS N 272 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE N 249 " --> pdb=" O LYS N 272 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA N 274 " --> pdb=" O ILE N 249 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ALA N 251 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL N 276 " --> pdb=" O ALA N 251 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= CR, first strand: chain 'N' and resid 476 through 479 3329 hydrogen bonds defined for protein. 9591 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: 18.65 Time building geometry restraints manager: 17.33 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: 18543 1.34 - 1.46: 8010 1.46 - 1.58: 27768 1.58 - 1.70: 55 1.70 - 1.82: 518 Bond restraints: 54894 Sorted by residual: bond pdb=" CB VAL K 38 " pdb=" CG1 VAL K 38 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CG1 ILE N 60 " pdb=" CD1 ILE N 60 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.54e+00 bond pdb=" CD GLU G 164 " pdb=" OE1 GLU G 164 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.33e+00 bond pdb=" CD GLU N 164 " pdb=" OE1 GLU N 164 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.26e+00 bond pdb=" CD GLU K 164 " pdb=" OE1 GLU K 164 " ideal model delta sigma weight residual 1.249 1.222 0.027 1.90e-02 2.77e+03 2.09e+00 ... (remaining 54889 not shown) Histogram of bond angle deviations from ideal: 97.06 - 105.61: 1039 105.61 - 114.17: 33311 114.17 - 122.72: 34971 122.72 - 131.28: 4849 131.28 - 139.83: 44 Bond angle restraints: 74214 Sorted by residual: angle pdb=" N GLU D 164 " pdb=" CA GLU D 164 " pdb=" CB GLU D 164 " ideal model delta sigma weight residual 110.16 116.92 -6.76 1.48e+00 4.57e-01 2.08e+01 angle pdb=" N GLU B 164 " pdb=" CA GLU B 164 " pdb=" CB GLU B 164 " ideal model delta sigma weight residual 110.16 116.85 -6.69 1.48e+00 4.57e-01 2.04e+01 angle pdb=" N GLU H 164 " pdb=" CA GLU H 164 " pdb=" CB GLU H 164 " ideal model delta sigma weight residual 110.16 116.83 -6.67 1.48e+00 4.57e-01 2.03e+01 angle pdb=" N GLU A 164 " pdb=" CA GLU A 164 " pdb=" CB GLU A 164 " ideal model delta sigma weight residual 110.16 116.77 -6.61 1.48e+00 4.57e-01 1.99e+01 angle pdb=" N GLU E 164 " pdb=" CA GLU E 164 " pdb=" CB GLU E 164 " ideal model delta sigma weight residual 110.16 116.65 -6.49 1.48e+00 4.57e-01 1.92e+01 ... (remaining 74209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 31200 17.97 - 35.93: 2516 35.93 - 53.90: 461 53.90 - 71.87: 98 71.87 - 89.83: 25 Dihedral angle restraints: 34300 sinusoidal: 13566 harmonic: 20734 Sorted by residual: dihedral pdb=" CA ASP D 41 " pdb=" C ASP D 41 " pdb=" N LYS D 42 " pdb=" CA LYS D 42 " ideal model delta harmonic sigma weight residual 180.00 148.44 31.56 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA ASP E 41 " pdb=" C ASP E 41 " pdb=" N LYS E 42 " pdb=" CA LYS E 42 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASP F 41 " pdb=" C ASP F 41 " pdb=" N LYS F 42 " pdb=" CA LYS F 42 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 34297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 5782 0.037 - 0.074: 2040 0.074 - 0.110: 852 0.110 - 0.147: 289 0.147 - 0.184: 39 Chirality restraints: 9002 Sorted by residual: chirality pdb=" CB VAL C 39 " pdb=" CA VAL C 39 " pdb=" CG1 VAL C 39 " pdb=" CG2 VAL C 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA GLU G 164 " pdb=" N GLU G 164 " pdb=" C GLU G 164 " pdb=" CB GLU G 164 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA GLU L 164 " pdb=" N GLU L 164 " pdb=" C GLU L 164 " pdb=" CB GLU L 164 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 8999 not shown) Planarity restraints: 9632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 311 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C LYS E 311 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS E 311 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA E 312 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP M 41 " -0.008 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" CG ASP M 41 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP M 41 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP M 41 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET N 514 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C MET N 514 " 0.029 2.00e-02 2.50e+03 pdb=" O MET N 514 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE N 515 " -0.010 2.00e-02 2.50e+03 ... (remaining 9629 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 13368 2.80 - 3.32: 56185 3.32 - 3.85: 96248 3.85 - 4.37: 110071 4.37 - 4.90: 183480 Nonbonded interactions: 459352 Sorted by model distance: nonbonded pdb=" OD2 ASP H 41 " pdb=" NZ LYS N 4 " model vdw 2.270 2.520 nonbonded pdb=" OG1 THR E 90 " pdb=" O2B ATP E 601 " model vdw 2.290 2.440 nonbonded pdb=" NZ LYS L 4 " pdb=" OE1 GLU M 59 " model vdw 2.298 2.520 nonbonded pdb=" OG1 THR F 90 " pdb=" O2B ATP F 601 " model vdw 2.316 2.440 nonbonded pdb=" O GLU A 397 " pdb=" ND1 HIS A 401 " model vdw 2.321 2.520 ... (remaining 459347 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: 2.440 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: 0.050 Extract box with map and model: 13.240 Check model and map are aligned: 0.590 Set scattering table: 0.380 Process input model: 112.800 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 54894 Z= 0.256 Angle : 0.782 9.839 74214 Z= 0.434 Chirality : 0.048 0.184 9002 Planarity : 0.005 0.038 9632 Dihedral : 13.646 89.832 21000 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.37 (0.09), residues: 7322 helix: 0.20 (0.07), residues: 4088 sheet: -0.29 (0.15), residues: 1050 loop : -0.81 (0.11), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 401 PHE 0.014 0.002 PHE G 195 TYR 0.020 0.001 TYR G 203 ARG 0.005 0.001 ARG D 18 *********************** 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 597 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 597 time to evaluate : 5.099 Fit side-chains revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8568 (t) cc_final: 0.8346 (t) REVERT: A 517 THR cc_start: 0.9453 (m) cc_final: 0.9060 (p) REVERT: B 401 HIS cc_start: 0.8782 (m90) cc_final: 0.8534 (m90) REVERT: B 514 MET cc_start: 0.8404 (ttm) cc_final: 0.7556 (ttm) REVERT: B 517 THR cc_start: 0.9416 (m) cc_final: 0.8994 (p) REVERT: C 22 VAL cc_start: 0.8793 (t) cc_final: 0.8548 (t) REVERT: C 111 MET cc_start: 0.7140 (mmm) cc_final: 0.6520 (tpt) REVERT: C 307 MET cc_start: 0.8558 (pmm) cc_final: 0.8267 (pmm) REVERT: C 400 LEU cc_start: 0.9449 (tp) cc_final: 0.9129 (pp) REVERT: C 488 MET cc_start: 0.8094 (mmt) cc_final: 0.7445 (mmp) REVERT: F 111 MET cc_start: 0.7366 (mmm) cc_final: 0.6643 (mmt) REVERT: G 488 MET cc_start: 0.7753 (tpt) cc_final: 0.7231 (tpt) REVERT: H 22 VAL cc_start: 0.8550 (t) cc_final: 0.8316 (t) REVERT: H 69 MET cc_start: 0.8807 (mtp) cc_final: 0.8427 (mmm) REVERT: H 114 MET cc_start: 0.6610 (tmm) cc_final: 0.6372 (tmm) REVERT: H 488 MET cc_start: 0.7959 (mmp) cc_final: 0.7631 (mmt) REVERT: H 517 THR cc_start: 0.9409 (m) cc_final: 0.9049 (p) REVERT: I 64 ASP cc_start: 0.7973 (t0) cc_final: 0.7686 (t0) REVERT: I 166 MET cc_start: 0.9333 (tmm) cc_final: 0.9068 (tpt) REVERT: I 488 MET cc_start: 0.8254 (mmt) cc_final: 0.7846 (mmp) REVERT: J 307 MET cc_start: 0.8499 (pmm) cc_final: 0.8295 (pmm) REVERT: J 400 LEU cc_start: 0.9340 (tp) cc_final: 0.9133 (pp) REVERT: K 514 MET cc_start: 0.8547 (ttm) cc_final: 0.8297 (ttm) REVERT: K 517 THR cc_start: 0.9492 (m) cc_final: 0.9024 (p) REVERT: L 307 MET cc_start: 0.8132 (pmm) cc_final: 0.7778 (pmm) REVERT: L 400 LEU cc_start: 0.9319 (tp) cc_final: 0.9047 (pp) REVERT: L 514 MET cc_start: 0.8592 (ttm) cc_final: 0.8313 (ttm) REVERT: L 517 THR cc_start: 0.9348 (m) cc_final: 0.8960 (p) REVERT: M 267 MET cc_start: 0.6485 (mmm) cc_final: 0.5984 (ptt) REVERT: M 488 MET cc_start: 0.7970 (mmt) cc_final: 0.7051 (mmp) REVERT: N 114 MET cc_start: 0.6736 (tmm) cc_final: 0.6288 (tmm) REVERT: N 488 MET cc_start: 0.7626 (tpt) cc_final: 0.7164 (tpt) REVERT: N 520 MET cc_start: 0.6640 (ttt) cc_final: 0.6239 (ttt) outliers start: 0 outliers final: 0 residues processed: 597 average time/residue: 0.4543 time to fit residues: 479.4432 Evaluate side-chains 447 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 447 time to evaluate : 4.569 ------------------------------------------------------------------------------- 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: 10.0000 chunk 551 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 372 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 570 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 346 optimal weight: 10.0000 chunk 424 optimal weight: 6.9990 chunk 661 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 457 ASN ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1374 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= 0.420 Angle : 0.642 6.916 74214 Z= 0.352 Chirality : 0.044 0.142 9002 Planarity : 0.004 0.038 9632 Dihedral : 8.592 77.362 8218 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.64 % Allowed : 6.22 % Favored : 93.14 % 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: 0.27 (0.09), residues: 7322 helix: 0.82 (0.08), residues: 4102 sheet: -0.32 (0.15), residues: 1050 loop : -0.59 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS I 401 PHE 0.014 0.002 PHE F 195 TYR 0.012 0.002 TYR L 476 ARG 0.009 0.001 ARG C 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 498 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 462 time to evaluate : 4.626 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: A 114 MET cc_start: 0.7125 (tmm) cc_final: 0.6849 (tmm) REVERT: B 419 LEU cc_start: 0.9387 (mt) cc_final: 0.9141 (mp) REVERT: C 111 MET cc_start: 0.7690 (mmm) cc_final: 0.7162 (mmm) REVERT: C 114 MET cc_start: 0.7087 (tmm) cc_final: 0.6663 (tmm) REVERT: C 307 MET cc_start: 0.8677 (pmm) cc_final: 0.8443 (pmm) REVERT: C 488 MET cc_start: 0.8298 (mmt) cc_final: 0.7895 (mmp) REVERT: E 41 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7124 (p0) REVERT: E 307 MET cc_start: 0.8683 (pmm) cc_final: 0.8449 (pmm) REVERT: E 488 MET cc_start: 0.8283 (mmt) cc_final: 0.7551 (mmt) REVERT: F 114 MET cc_start: 0.7130 (tmm) cc_final: 0.6734 (tmm) REVERT: G 488 MET cc_start: 0.8171 (tpt) cc_final: 0.7774 (mmm) REVERT: G 519 CYS cc_start: 0.7064 (m) cc_final: 0.6338 (t) REVERT: H 114 MET cc_start: 0.7123 (tmm) cc_final: 0.6662 (tmm) REVERT: H 488 MET cc_start: 0.8244 (mmp) cc_final: 0.7571 (mmt) REVERT: I 114 MET cc_start: 0.7173 (tmm) cc_final: 0.6798 (tmm) REVERT: I 488 MET cc_start: 0.8644 (mmt) cc_final: 0.8155 (mmt) REVERT: J 400 LEU cc_start: 0.9482 (tp) cc_final: 0.9271 (pp) REVERT: J 488 MET cc_start: 0.8245 (mmt) cc_final: 0.7798 (mmp) REVERT: K 114 MET cc_start: 0.7095 (tmm) cc_final: 0.6755 (tmm) REVERT: L 114 MET cc_start: 0.7179 (tmm) cc_final: 0.6811 (tmm) REVERT: L 307 MET cc_start: 0.8094 (pmm) cc_final: 0.7784 (pmm) REVERT: M 22 VAL cc_start: 0.8858 (t) cc_final: 0.8502 (t) REVERT: M 111 MET cc_start: 0.7939 (mmm) cc_final: 0.7696 (mmm) REVERT: M 114 MET cc_start: 0.7108 (tmm) cc_final: 0.6792 (tmm) REVERT: M 267 MET cc_start: 0.6440 (mmm) cc_final: 0.5901 (ptt) REVERT: M 488 MET cc_start: 0.8305 (mmt) cc_final: 0.7823 (mmt) REVERT: N 111 MET cc_start: 0.6660 (tpp) cc_final: 0.6389 (mmm) REVERT: N 114 MET cc_start: 0.7001 (tmm) cc_final: 0.6551 (tmm) REVERT: N 488 MET cc_start: 0.8074 (tpt) cc_final: 0.7669 (mmm) outliers start: 36 outliers final: 27 residues processed: 495 average time/residue: 0.4603 time to fit residues: 402.0970 Evaluate side-chains 426 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 398 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 0.8980 chunk 205 optimal weight: 9.9990 chunk 550 optimal weight: 3.9990 chunk 450 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 662 optimal weight: 0.6980 chunk 715 optimal weight: 0.9990 chunk 589 optimal weight: 7.9990 chunk 656 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 531 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 72 GLN ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN N 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54894 Z= 0.169 Angle : 0.499 7.090 74214 Z= 0.271 Chirality : 0.041 0.151 9002 Planarity : 0.003 0.045 9632 Dihedral : 8.315 74.611 8218 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: 0.80 (0.10), residues: 7322 helix: 1.31 (0.08), residues: 4116 sheet: -0.24 (0.15), residues: 1050 loop : -0.45 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 401 PHE 0.012 0.001 PHE G 195 TYR 0.006 0.001 TYR B 203 ARG 0.005 0.000 ARG D 13 *********************** 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 540 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 540 time to evaluate : 4.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6941 (tmm) cc_final: 0.6657 (tmm) REVERT: A 488 MET cc_start: 0.8185 (mmt) cc_final: 0.7476 (mmt) REVERT: A 517 THR cc_start: 0.9523 (m) cc_final: 0.9271 (p) REVERT: B 114 MET cc_start: 0.6991 (tmm) cc_final: 0.6708 (tmm) REVERT: B 517 THR cc_start: 0.9482 (m) cc_final: 0.9161 (p) REVERT: C 114 MET cc_start: 0.7011 (tmm) cc_final: 0.6641 (tmm) REVERT: C 307 MET cc_start: 0.8619 (pmm) cc_final: 0.8365 (pmm) REVERT: C 400 LEU cc_start: 0.9502 (tp) cc_final: 0.9207 (pp) REVERT: D 16 MET cc_start: 0.8249 (mtm) cc_final: 0.7949 (mtp) REVERT: D 401 HIS cc_start: 0.8821 (m90) cc_final: 0.8600 (m90) REVERT: E 307 MET cc_start: 0.8734 (pmm) cc_final: 0.8514 (pmm) REVERT: E 488 MET cc_start: 0.8049 (mmt) cc_final: 0.7642 (mmt) REVERT: F 16 MET cc_start: 0.7456 (ptp) cc_final: 0.6857 (mtm) REVERT: F 22 VAL cc_start: 0.8482 (t) cc_final: 0.8109 (t) REVERT: F 519 CYS cc_start: 0.5910 (t) cc_final: 0.5670 (t) REVERT: G 22 VAL cc_start: 0.8892 (t) cc_final: 0.8480 (t) REVERT: G 111 MET cc_start: 0.6853 (mmm) cc_final: 0.6518 (mmm) REVERT: G 488 MET cc_start: 0.8145 (tpt) cc_final: 0.7769 (mmm) REVERT: H 114 MET cc_start: 0.6948 (tmm) cc_final: 0.6565 (tmm) REVERT: H 488 MET cc_start: 0.7963 (mmp) cc_final: 0.7589 (mmt) REVERT: H 517 THR cc_start: 0.9490 (m) cc_final: 0.9202 (p) REVERT: I 114 MET cc_start: 0.7093 (tmm) cc_final: 0.6695 (tmm) REVERT: I 400 LEU cc_start: 0.9389 (tp) cc_final: 0.9144 (pp) REVERT: I 488 MET cc_start: 0.8552 (mmt) cc_final: 0.8241 (mmt) REVERT: J 307 MET cc_start: 0.8498 (pmm) cc_final: 0.8282 (pmm) REVERT: K 114 MET cc_start: 0.6994 (tmm) cc_final: 0.6652 (tmm) REVERT: K 517 THR cc_start: 0.9651 (m) cc_final: 0.9276 (p) REVERT: L 69 MET cc_start: 0.8809 (mtp) cc_final: 0.8564 (mtp) REVERT: L 114 MET cc_start: 0.7068 (tmm) cc_final: 0.6714 (tmm) REVERT: L 307 MET cc_start: 0.8071 (pmm) cc_final: 0.7755 (pmm) REVERT: L 400 LEU cc_start: 0.9346 (tp) cc_final: 0.9080 (pp) REVERT: L 401 HIS cc_start: 0.8475 (m90) cc_final: 0.8260 (m90) REVERT: L 488 MET cc_start: 0.8093 (mmt) cc_final: 0.7773 (mmt) REVERT: L 517 THR cc_start: 0.9488 (m) cc_final: 0.9142 (p) REVERT: L 520 MET cc_start: 0.7196 (ttt) cc_final: 0.6977 (ttt) REVERT: M 22 VAL cc_start: 0.8760 (t) cc_final: 0.8340 (t) REVERT: M 111 MET cc_start: 0.7547 (mmm) cc_final: 0.7269 (mmm) REVERT: M 114 MET cc_start: 0.6961 (tmm) cc_final: 0.6727 (tmm) REVERT: M 267 MET cc_start: 0.6486 (mmm) cc_final: 0.5946 (ptt) REVERT: M 400 LEU cc_start: 0.9382 (tp) cc_final: 0.9179 (pp) REVERT: M 488 MET cc_start: 0.8328 (mmt) cc_final: 0.7956 (mmt) REVERT: N 22 VAL cc_start: 0.8820 (t) cc_final: 0.8448 (t) REVERT: N 488 MET cc_start: 0.7982 (tpt) cc_final: 0.7671 (mmm) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 0.4549 time to fit residues: 433.6319 Evaluate side-chains 430 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 4.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 20.0000 chunk 497 optimal weight: 30.0000 chunk 343 optimal weight: 30.0000 chunk 73 optimal weight: 0.3980 chunk 316 optimal weight: 2.9990 chunk 444 optimal weight: 3.9990 chunk 664 optimal weight: 0.0000 chunk 703 optimal weight: 6.9990 chunk 347 optimal weight: 20.0000 chunk 629 optimal weight: 2.9990 chunk 189 optimal weight: 0.4980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 457 ASN ** 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: 0.7915 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 54894 Z= 0.163 Angle : 0.487 6.359 74214 Z= 0.264 Chirality : 0.040 0.146 9002 Planarity : 0.003 0.026 9632 Dihedral : 7.922 68.447 8218 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.10), residues: 7322 helix: 1.49 (0.08), residues: 4116 sheet: -0.16 (0.15), residues: 1050 loop : -0.35 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 401 PHE 0.010 0.001 PHE L 195 TYR 0.006 0.001 TYR D 476 ARG 0.006 0.000 ARG M 18 *********************** 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 536 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 4.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6966 (tmm) cc_final: 0.6677 (tmm) REVERT: A 517 THR cc_start: 0.9512 (m) cc_final: 0.9193 (t) REVERT: B 114 MET cc_start: 0.6960 (tmm) cc_final: 0.6654 (tmm) REVERT: B 517 THR cc_start: 0.9485 (m) cc_final: 0.9030 (p) REVERT: B 520 MET cc_start: 0.6022 (mtp) cc_final: 0.5709 (mtp) REVERT: C 114 MET cc_start: 0.6991 (tmm) cc_final: 0.6620 (tmm) REVERT: C 203 TYR cc_start: 0.8382 (m-10) cc_final: 0.8094 (m-80) REVERT: C 307 MET cc_start: 0.8629 (pmm) cc_final: 0.8357 (pmm) REVERT: C 400 LEU cc_start: 0.9507 (tp) cc_final: 0.9213 (pp) REVERT: E 400 LEU cc_start: 0.9349 (tp) cc_final: 0.9135 (pp) REVERT: E 488 MET cc_start: 0.8060 (mmt) cc_final: 0.7520 (mmt) REVERT: F 519 CYS cc_start: 0.5914 (t) cc_final: 0.5702 (t) REVERT: G 22 VAL cc_start: 0.8829 (t) cc_final: 0.8436 (t) REVERT: G 111 MET cc_start: 0.6960 (mmm) cc_final: 0.6455 (mmt) REVERT: G 488 MET cc_start: 0.8216 (tpt) cc_final: 0.7788 (mmm) REVERT: H 114 MET cc_start: 0.6962 (tmm) cc_final: 0.6540 (tmm) REVERT: H 488 MET cc_start: 0.7929 (mmp) cc_final: 0.7551 (mmt) REVERT: H 517 THR cc_start: 0.9453 (m) cc_final: 0.9156 (p) REVERT: I 114 MET cc_start: 0.7133 (tmm) cc_final: 0.6713 (tmm) REVERT: I 400 LEU cc_start: 0.9390 (tp) cc_final: 0.9150 (pp) REVERT: I 488 MET cc_start: 0.8629 (mmt) cc_final: 0.8279 (mmt) REVERT: J 25 ASP cc_start: 0.7802 (m-30) cc_final: 0.7545 (m-30) REVERT: K 114 MET cc_start: 0.6948 (tmm) cc_final: 0.6598 (tmm) REVERT: K 514 MET cc_start: 0.8465 (ttm) cc_final: 0.8243 (ttm) REVERT: K 517 THR cc_start: 0.9634 (m) cc_final: 0.9237 (p) REVERT: L 114 MET cc_start: 0.7105 (tmm) cc_final: 0.6758 (tmm) REVERT: L 307 MET cc_start: 0.8201 (pmm) cc_final: 0.7905 (pmm) REVERT: L 400 LEU cc_start: 0.9361 (tp) cc_final: 0.9110 (pp) REVERT: L 488 MET cc_start: 0.8041 (mmt) cc_final: 0.7789 (mmt) REVERT: L 517 THR cc_start: 0.9485 (m) cc_final: 0.9079 (p) REVERT: L 520 MET cc_start: 0.6526 (mtp) cc_final: 0.6281 (mtp) REVERT: M 16 MET cc_start: 0.8454 (mtm) cc_final: 0.8079 (mtp) REVERT: M 22 VAL cc_start: 0.8709 (t) cc_final: 0.8361 (t) REVERT: M 114 MET cc_start: 0.7035 (tmm) cc_final: 0.6801 (tmm) REVERT: M 267 MET cc_start: 0.6611 (mmm) cc_final: 0.6082 (ptp) REVERT: M 488 MET cc_start: 0.8335 (mmt) cc_final: 0.8049 (mmt) REVERT: N 22 VAL cc_start: 0.8800 (t) cc_final: 0.8431 (t) REVERT: N 69 MET cc_start: 0.8726 (mtp) cc_final: 0.8449 (mtp) REVERT: N 488 MET cc_start: 0.7947 (tpt) cc_final: 0.7562 (mmm) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.4591 time to fit residues: 437.0866 Evaluate side-chains 433 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 10 optimal weight: 4.9990 chunk 523 optimal weight: 0.9990 chunk 290 optimal weight: 40.0000 chunk 600 optimal weight: 20.0000 chunk 486 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 9.9990 chunk 631 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54894 Z= 0.228 Angle : 0.506 6.747 74214 Z= 0.273 Chirality : 0.041 0.143 9002 Planarity : 0.003 0.030 9632 Dihedral : 7.755 75.546 8218 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 7322 helix: 1.51 (0.08), residues: 4200 sheet: -0.15 (0.15), residues: 1050 loop : -0.51 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 401 PHE 0.010 0.001 PHE L 195 TYR 0.007 0.001 TYR D 476 ARG 0.005 0.000 ARG D 13 *********************** 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 516 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 4.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8525 (t) cc_final: 0.8298 (t) REVERT: A 114 MET cc_start: 0.6969 (tmm) cc_final: 0.6708 (tmm) REVERT: B 114 MET cc_start: 0.7019 (tmm) cc_final: 0.6646 (tmm) REVERT: C 22 VAL cc_start: 0.8611 (t) cc_final: 0.8402 (t) REVERT: C 114 MET cc_start: 0.6981 (tmm) cc_final: 0.6609 (tmm) REVERT: C 203 TYR cc_start: 0.8400 (m-10) cc_final: 0.8101 (m-80) REVERT: C 307 MET cc_start: 0.8628 (pmm) cc_final: 0.8349 (pmm) REVERT: C 400 LEU cc_start: 0.9528 (tp) cc_final: 0.9249 (pp) REVERT: D 400 LEU cc_start: 0.9434 (tp) cc_final: 0.9215 (pp) REVERT: E 488 MET cc_start: 0.8162 (mmt) cc_final: 0.7526 (mmt) REVERT: F 520 MET cc_start: 0.6605 (ttt) cc_final: 0.6390 (ttt) REVERT: G 22 VAL cc_start: 0.8851 (t) cc_final: 0.8437 (t) REVERT: G 111 MET cc_start: 0.7149 (mmm) cc_final: 0.6747 (mmm) REVERT: G 488 MET cc_start: 0.8362 (tpt) cc_final: 0.7863 (mmm) REVERT: H 114 MET cc_start: 0.7020 (tmm) cc_final: 0.6599 (tmm) REVERT: H 488 MET cc_start: 0.7982 (mmp) cc_final: 0.7561 (mmt) REVERT: H 517 THR cc_start: 0.9467 (m) cc_final: 0.9113 (p) REVERT: I 114 MET cc_start: 0.7093 (tmm) cc_final: 0.6682 (tmm) REVERT: I 400 LEU cc_start: 0.9404 (tp) cc_final: 0.9174 (pp) REVERT: I 488 MET cc_start: 0.8705 (mmt) cc_final: 0.8247 (mmt) REVERT: I 520 MET cc_start: 0.6626 (mtp) cc_final: 0.6407 (mtp) REVERT: J 25 ASP cc_start: 0.7736 (m-30) cc_final: 0.7510 (m-30) REVERT: J 488 MET cc_start: 0.8058 (mmt) cc_final: 0.7729 (mmt) REVERT: K 114 MET cc_start: 0.6953 (tmm) cc_final: 0.6548 (tmm) REVERT: K 514 MET cc_start: 0.8344 (ttm) cc_final: 0.8120 (ttm) REVERT: K 517 THR cc_start: 0.9640 (m) cc_final: 0.9257 (p) REVERT: L 16 MET cc_start: 0.8291 (mtm) cc_final: 0.7991 (mtp) REVERT: L 114 MET cc_start: 0.7130 (tmm) cc_final: 0.6714 (tmm) REVERT: L 307 MET cc_start: 0.8165 (pmm) cc_final: 0.7852 (pmm) REVERT: L 400 LEU cc_start: 0.9370 (tp) cc_final: 0.9133 (pp) REVERT: L 488 MET cc_start: 0.8139 (mmt) cc_final: 0.7833 (mmt) REVERT: L 520 MET cc_start: 0.6892 (mtp) cc_final: 0.5888 (mtp) REVERT: M 16 MET cc_start: 0.8389 (mtm) cc_final: 0.8111 (mtp) REVERT: M 22 VAL cc_start: 0.8734 (t) cc_final: 0.8343 (t) REVERT: M 111 MET cc_start: 0.7524 (mmm) cc_final: 0.7061 (mmm) REVERT: M 114 MET cc_start: 0.7052 (tmm) cc_final: 0.6819 (tmm) REVERT: M 267 MET cc_start: 0.6436 (mmm) cc_final: 0.5903 (ptt) REVERT: M 488 MET cc_start: 0.8367 (mmt) cc_final: 0.8085 (mmt) REVERT: N 22 VAL cc_start: 0.8815 (t) cc_final: 0.8386 (t) REVERT: N 69 MET cc_start: 0.8612 (mtp) cc_final: 0.8412 (mtp) REVERT: N 488 MET cc_start: 0.8218 (tpt) cc_final: 0.7678 (mmm) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.4658 time to fit residues: 425.7145 Evaluate side-chains 422 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 4.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 4.9990 chunk 633 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 413 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 704 optimal weight: 7.9990 chunk 584 optimal weight: 1.9990 chunk 326 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 232 optimal weight: 9.9990 chunk 369 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 457 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 54894 Z= 0.148 Angle : 0.496 7.021 74214 Z= 0.266 Chirality : 0.040 0.143 9002 Planarity : 0.003 0.026 9632 Dihedral : 7.511 71.105 8218 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.10), residues: 7322 helix: 1.63 (0.08), residues: 4102 sheet: -0.08 (0.15), residues: 1050 loop : -0.17 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.021 0.001 PHE N 66 TYR 0.007 0.001 TYR J 203 ARG 0.004 0.000 ARG M 18 *********************** 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 548 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 4.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6949 (tmm) cc_final: 0.6656 (tmm) REVERT: A 517 THR cc_start: 0.9522 (m) cc_final: 0.9074 (t) REVERT: A 520 MET cc_start: 0.6480 (mtp) cc_final: 0.5578 (mtp) REVERT: B 114 MET cc_start: 0.6848 (tmm) cc_final: 0.6515 (tmm) REVERT: B 488 MET cc_start: 0.8274 (mmt) cc_final: 0.7898 (mmp) REVERT: B 514 MET cc_start: 0.8524 (ttm) cc_final: 0.8296 (ttm) REVERT: B 517 THR cc_start: 0.9452 (m) cc_final: 0.9095 (p) REVERT: C 114 MET cc_start: 0.6889 (tmm) cc_final: 0.6524 (tmm) REVERT: C 203 TYR cc_start: 0.8423 (m-10) cc_final: 0.8154 (m-80) REVERT: C 307 MET cc_start: 0.8565 (pmm) cc_final: 0.8258 (pmm) REVERT: C 389 MET cc_start: 0.8392 (mmp) cc_final: 0.8146 (mmp) REVERT: C 400 LEU cc_start: 0.9500 (tp) cc_final: 0.9223 (pp) REVERT: D 400 LEU cc_start: 0.9387 (tp) cc_final: 0.9164 (pp) REVERT: D 517 THR cc_start: 0.9669 (m) cc_final: 0.9304 (p) REVERT: E 400 LEU cc_start: 0.9328 (tp) cc_final: 0.9122 (pp) REVERT: E 488 MET cc_start: 0.8078 (mmt) cc_final: 0.7578 (mmt) REVERT: E 517 THR cc_start: 0.9551 (m) cc_final: 0.9187 (p) REVERT: F 517 THR cc_start: 0.9556 (m) cc_final: 0.9211 (p) REVERT: G 22 VAL cc_start: 0.8837 (t) cc_final: 0.8454 (t) REVERT: G 488 MET cc_start: 0.8264 (tpt) cc_final: 0.7785 (mmm) REVERT: H 111 MET cc_start: 0.6704 (mmt) cc_final: 0.6496 (mmt) REVERT: H 114 MET cc_start: 0.6889 (tmm) cc_final: 0.6507 (tmm) REVERT: H 488 MET cc_start: 0.7935 (mmp) cc_final: 0.7620 (mmt) REVERT: H 517 THR cc_start: 0.9455 (m) cc_final: 0.9148 (p) REVERT: I 114 MET cc_start: 0.6962 (tmm) cc_final: 0.6565 (tmm) REVERT: I 400 LEU cc_start: 0.9373 (tp) cc_final: 0.9165 (pp) REVERT: I 488 MET cc_start: 0.8582 (mmt) cc_final: 0.8209 (mmt) REVERT: J 25 ASP cc_start: 0.7748 (m-30) cc_final: 0.7523 (m-30) REVERT: J 307 MET cc_start: 0.8418 (pmm) cc_final: 0.8208 (pmm) REVERT: K 61 GLU cc_start: 0.7062 (pt0) cc_final: 0.6798 (mt-10) REVERT: K 114 MET cc_start: 0.6822 (tmm) cc_final: 0.6442 (tmm) REVERT: K 400 LEU cc_start: 0.9318 (tp) cc_final: 0.9071 (pp) REVERT: K 514 MET cc_start: 0.8320 (ttm) cc_final: 0.7992 (ttm) REVERT: K 517 THR cc_start: 0.9658 (m) cc_final: 0.9295 (p) REVERT: L 114 MET cc_start: 0.7119 (tmm) cc_final: 0.6642 (tmm) REVERT: L 307 MET cc_start: 0.8209 (pmm) cc_final: 0.7877 (pmm) REVERT: L 400 LEU cc_start: 0.9355 (tp) cc_final: 0.9104 (pp) REVERT: L 517 THR cc_start: 0.9450 (m) cc_final: 0.9089 (p) REVERT: M 22 VAL cc_start: 0.8663 (t) cc_final: 0.8267 (t) REVERT: M 114 MET cc_start: 0.6978 (tmm) cc_final: 0.6774 (tmm) REVERT: M 267 MET cc_start: 0.6471 (mmm) cc_final: 0.5871 (ptm) REVERT: M 488 MET cc_start: 0.8340 (mmt) cc_final: 0.8087 (mmt) REVERT: N 22 VAL cc_start: 0.8721 (t) cc_final: 0.8311 (t) REVERT: N 111 MET cc_start: 0.6570 (tpp) cc_final: 0.6347 (tpp) REVERT: N 488 MET cc_start: 0.8195 (tpt) cc_final: 0.7682 (mmm) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.4620 time to fit residues: 451.2048 Evaluate side-chains 423 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.7980 chunk 79 optimal weight: 40.0000 chunk 401 optimal weight: 30.0000 chunk 514 optimal weight: 2.9990 chunk 398 optimal weight: 5.9990 chunk 592 optimal weight: 8.9990 chunk 393 optimal weight: 30.0000 chunk 701 optimal weight: 10.0000 chunk 439 optimal weight: 2.9990 chunk 427 optimal weight: 0.9990 chunk 323 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 54894 Z= 0.218 Angle : 0.517 9.346 74214 Z= 0.279 Chirality : 0.041 0.142 9002 Planarity : 0.003 0.026 9632 Dihedral : 7.384 71.055 8218 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.10), residues: 7322 helix: 1.67 (0.08), residues: 4102 sheet: -0.08 (0.15), residues: 1050 loop : -0.24 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS H 401 PHE 0.013 0.001 PHE N 66 TYR 0.007 0.001 TYR E 476 ARG 0.004 0.000 ARG D 13 *********************** 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 513 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 4.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.7023 (tmm) cc_final: 0.6718 (tmm) REVERT: B 114 MET cc_start: 0.6876 (tmm) cc_final: 0.6512 (tmm) REVERT: B 488 MET cc_start: 0.8333 (mmt) cc_final: 0.7885 (mmp) REVERT: C 22 VAL cc_start: 0.8621 (t) cc_final: 0.8400 (t) REVERT: C 114 MET cc_start: 0.6904 (tmm) cc_final: 0.6556 (tmm) REVERT: C 203 TYR cc_start: 0.8440 (m-10) cc_final: 0.8148 (m-80) REVERT: C 307 MET cc_start: 0.8555 (pmm) cc_final: 0.8244 (pmm) REVERT: C 400 LEU cc_start: 0.9523 (tp) cc_final: 0.9237 (pp) REVERT: C 401 HIS cc_start: 0.8832 (m90) cc_final: 0.8623 (m90) REVERT: D 401 HIS cc_start: 0.8795 (m90) cc_final: 0.8581 (m90) REVERT: D 517 THR cc_start: 0.9614 (m) cc_final: 0.9226 (p) REVERT: E 488 MET cc_start: 0.8176 (mmt) cc_final: 0.7564 (mmt) REVERT: F 16 MET cc_start: 0.7953 (mtm) cc_final: 0.7443 (mtp) REVERT: G 22 VAL cc_start: 0.8834 (t) cc_final: 0.8440 (t) REVERT: G 111 MET cc_start: 0.6844 (mmt) cc_final: 0.6315 (mmm) REVERT: G 114 MET cc_start: 0.6694 (tmm) cc_final: 0.6395 (tmm) REVERT: G 488 MET cc_start: 0.8444 (tpt) cc_final: 0.7852 (mmm) REVERT: H 114 MET cc_start: 0.7001 (tmm) cc_final: 0.6568 (tmm) REVERT: H 488 MET cc_start: 0.7954 (mmp) cc_final: 0.7612 (mmt) REVERT: H 517 THR cc_start: 0.9489 (m) cc_final: 0.9165 (p) REVERT: I 114 MET cc_start: 0.7075 (tmm) cc_final: 0.6643 (tmm) REVERT: I 488 MET cc_start: 0.8655 (mmt) cc_final: 0.8188 (mmt) REVERT: J 25 ASP cc_start: 0.7722 (m-30) cc_final: 0.7517 (m-30) REVERT: J 111 MET cc_start: 0.7320 (mmm) cc_final: 0.6957 (mmm) REVERT: J 203 TYR cc_start: 0.8423 (m-10) cc_final: 0.8166 (m-80) REVERT: J 307 MET cc_start: 0.8410 (pmm) cc_final: 0.8203 (pmm) REVERT: K 114 MET cc_start: 0.6864 (tmm) cc_final: 0.6526 (tmm) REVERT: K 514 MET cc_start: 0.8225 (ttm) cc_final: 0.7969 (ttm) REVERT: K 517 THR cc_start: 0.9640 (m) cc_final: 0.9276 (p) REVERT: L 114 MET cc_start: 0.7159 (tmm) cc_final: 0.6724 (tmm) REVERT: L 307 MET cc_start: 0.8203 (pmm) cc_final: 0.7861 (pmm) REVERT: L 400 LEU cc_start: 0.9364 (tp) cc_final: 0.9133 (pp) REVERT: L 514 MET cc_start: 0.8672 (ttm) cc_final: 0.8394 (ttm) REVERT: L 517 THR cc_start: 0.9493 (m) cc_final: 0.9071 (p) REVERT: L 520 MET cc_start: 0.6452 (mtp) cc_final: 0.6177 (mtp) REVERT: M 22 VAL cc_start: 0.8698 (t) cc_final: 0.8318 (t) REVERT: M 114 MET cc_start: 0.7067 (tmm) cc_final: 0.6826 (tmm) REVERT: M 267 MET cc_start: 0.6447 (mmm) cc_final: 0.5954 (mtp) REVERT: M 488 MET cc_start: 0.8348 (mmt) cc_final: 0.8076 (mmt) REVERT: N 22 VAL cc_start: 0.8755 (t) cc_final: 0.8323 (t) REVERT: N 69 MET cc_start: 0.8520 (mtp) cc_final: 0.8245 (mtp) REVERT: N 488 MET cc_start: 0.8272 (tpt) cc_final: 0.7720 (mmm) REVERT: N 517 THR cc_start: 0.9429 (p) cc_final: 0.9203 (p) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.4677 time to fit residues: 425.3504 Evaluate side-chains 428 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 4.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 419 optimal weight: 0.7980 chunk 211 optimal weight: 0.9980 chunk 137 optimal weight: 30.0000 chunk 135 optimal weight: 20.0000 chunk 446 optimal weight: 9.9990 chunk 478 optimal weight: 0.9980 chunk 346 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 551 optimal weight: 0.0060 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 54894 Z= 0.143 Angle : 0.493 7.501 74214 Z= 0.263 Chirality : 0.040 0.141 9002 Planarity : 0.003 0.032 9632 Dihedral : 7.114 69.396 8218 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.10), residues: 7322 helix: 1.80 (0.08), residues: 4074 sheet: -0.01 (0.15), residues: 1050 loop : -0.17 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 401 PHE 0.012 0.001 PHE G 195 TYR 0.007 0.001 TYR L 203 ARG 0.012 0.000 ARG D 36 *********************** 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 545 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 4.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8468 (t) cc_final: 0.8237 (t) REVERT: A 114 MET cc_start: 0.6919 (tmm) cc_final: 0.6672 (tmm) REVERT: B 114 MET cc_start: 0.6824 (tmm) cc_final: 0.6481 (tmm) REVERT: B 517 THR cc_start: 0.9446 (m) cc_final: 0.9092 (p) REVERT: C 114 MET cc_start: 0.6864 (tmm) cc_final: 0.6493 (tmm) REVERT: C 203 TYR cc_start: 0.8449 (m-10) cc_final: 0.8127 (m-80) REVERT: C 307 MET cc_start: 0.8535 (pmm) cc_final: 0.8225 (pmm) REVERT: C 389 MET cc_start: 0.8368 (mmp) cc_final: 0.8109 (mmp) REVERT: C 400 LEU cc_start: 0.9496 (tp) cc_final: 0.9218 (pp) REVERT: D 517 THR cc_start: 0.9603 (m) cc_final: 0.9254 (p) REVERT: E 307 MET cc_start: 0.8858 (pmm) cc_final: 0.8620 (pmm) REVERT: E 488 MET cc_start: 0.8039 (mmt) cc_final: 0.7587 (mmt) REVERT: E 517 THR cc_start: 0.9529 (m) cc_final: 0.9161 (p) REVERT: F 517 THR cc_start: 0.9505 (m) cc_final: 0.9245 (p) REVERT: G 22 VAL cc_start: 0.8805 (t) cc_final: 0.8441 (t) REVERT: G 114 MET cc_start: 0.6637 (tmm) cc_final: 0.6336 (tmm) REVERT: G 288 MET cc_start: 0.9462 (ppp) cc_final: 0.9111 (ppp) REVERT: G 488 MET cc_start: 0.8294 (tpt) cc_final: 0.7752 (mmm) REVERT: H 114 MET cc_start: 0.6790 (tmm) cc_final: 0.6405 (tmm) REVERT: H 488 MET cc_start: 0.7953 (mmp) cc_final: 0.7662 (mmt) REVERT: H 514 MET cc_start: 0.8367 (ttm) cc_final: 0.7916 (ttm) REVERT: H 517 THR cc_start: 0.9461 (m) cc_final: 0.9143 (p) REVERT: I 114 MET cc_start: 0.6952 (tmm) cc_final: 0.6545 (tmm) REVERT: I 400 LEU cc_start: 0.9366 (tp) cc_final: 0.9156 (pp) REVERT: I 488 MET cc_start: 0.8550 (mmt) cc_final: 0.8211 (mmt) REVERT: J 25 ASP cc_start: 0.7733 (m-30) cc_final: 0.7519 (m-30) REVERT: J 203 TYR cc_start: 0.8439 (m-10) cc_final: 0.8146 (m-80) REVERT: J 307 MET cc_start: 0.8409 (pmm) cc_final: 0.8198 (pmm) REVERT: K 114 MET cc_start: 0.6755 (tmm) cc_final: 0.6427 (tmm) REVERT: K 400 LEU cc_start: 0.9322 (tp) cc_final: 0.9085 (pp) REVERT: K 514 MET cc_start: 0.8291 (ttm) cc_final: 0.7957 (ttm) REVERT: K 517 THR cc_start: 0.9659 (m) cc_final: 0.9313 (p) REVERT: L 114 MET cc_start: 0.7111 (tmm) cc_final: 0.6663 (tmm) REVERT: L 307 MET cc_start: 0.8188 (pmm) cc_final: 0.7860 (pmm) REVERT: L 400 LEU cc_start: 0.9348 (tp) cc_final: 0.9100 (pp) REVERT: L 514 MET cc_start: 0.8723 (ttm) cc_final: 0.8433 (ttm) REVERT: L 517 THR cc_start: 0.9383 (m) cc_final: 0.9039 (p) REVERT: M 22 VAL cc_start: 0.8665 (t) cc_final: 0.8247 (t) REVERT: M 267 MET cc_start: 0.6488 (mmm) cc_final: 0.5937 (mtp) REVERT: M 488 MET cc_start: 0.8331 (mmt) cc_final: 0.8100 (mmt) REVERT: M 517 THR cc_start: 0.9466 (m) cc_final: 0.9138 (p) REVERT: N 111 MET cc_start: 0.6538 (tpp) cc_final: 0.6052 (tpp) REVERT: N 488 MET cc_start: 0.8200 (tpt) cc_final: 0.7520 (mmm) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.4492 time to fit residues: 434.8925 Evaluate side-chains 430 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 4.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 0.9980 chunk 672 optimal weight: 0.9980 chunk 613 optimal weight: 0.0570 chunk 653 optimal weight: 20.0000 chunk 393 optimal weight: 30.0000 chunk 284 optimal weight: 8.9990 chunk 513 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 590 optimal weight: 8.9990 chunk 618 optimal weight: 5.9990 chunk 651 optimal weight: 50.0000 overall best weight: 1.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54894 Z= 0.183 Angle : 0.521 8.750 74214 Z= 0.280 Chirality : 0.041 0.152 9002 Planarity : 0.003 0.032 9632 Dihedral : 6.986 69.233 8218 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 1.41 (0.10), residues: 7322 helix: 1.81 (0.08), residues: 4046 sheet: -0.01 (0.15), residues: 1050 loop : -0.11 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 401 PHE 0.012 0.001 PHE G 195 TYR 0.008 0.001 TYR K 203 ARG 0.003 0.000 ARG D 13 *********************** 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 536 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 4.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6960 (tmm) cc_final: 0.6647 (tmm) REVERT: A 514 MET cc_start: 0.8444 (ttm) cc_final: 0.7965 (ttm) REVERT: A 517 THR cc_start: 0.9467 (m) cc_final: 0.9166 (p) REVERT: B 114 MET cc_start: 0.6859 (tmm) cc_final: 0.6504 (tmm) REVERT: B 488 MET cc_start: 0.8270 (mmt) cc_final: 0.7784 (mmp) REVERT: B 514 MET cc_start: 0.8515 (ttm) cc_final: 0.8307 (ttm) REVERT: B 517 THR cc_start: 0.9415 (m) cc_final: 0.9039 (p) REVERT: C 22 VAL cc_start: 0.8613 (t) cc_final: 0.8404 (t) REVERT: C 114 MET cc_start: 0.6919 (tmm) cc_final: 0.6559 (tmm) REVERT: C 203 TYR cc_start: 0.8431 (m-10) cc_final: 0.8139 (m-80) REVERT: C 307 MET cc_start: 0.8537 (pmm) cc_final: 0.8221 (pmm) REVERT: C 389 MET cc_start: 0.8348 (mmp) cc_final: 0.8099 (mmp) REVERT: C 400 LEU cc_start: 0.9514 (tp) cc_final: 0.9235 (pp) REVERT: D 400 LEU cc_start: 0.9396 (tp) cc_final: 0.9186 (pp) REVERT: D 401 HIS cc_start: 0.8795 (m90) cc_final: 0.8585 (m90) REVERT: D 517 THR cc_start: 0.9611 (m) cc_final: 0.9222 (p) REVERT: E 307 MET cc_start: 0.8857 (pmm) cc_final: 0.8634 (pmm) REVERT: E 488 MET cc_start: 0.8127 (mmt) cc_final: 0.7616 (mmt) REVERT: E 517 THR cc_start: 0.9506 (m) cc_final: 0.9100 (p) REVERT: F 514 MET cc_start: 0.8751 (ttp) cc_final: 0.8525 (ttm) REVERT: F 517 THR cc_start: 0.9574 (m) cc_final: 0.9188 (p) REVERT: G 22 VAL cc_start: 0.8794 (t) cc_final: 0.8424 (t) REVERT: G 288 MET cc_start: 0.9456 (ppp) cc_final: 0.9161 (ppp) REVERT: G 488 MET cc_start: 0.8384 (tpt) cc_final: 0.7761 (mmm) REVERT: H 111 MET cc_start: 0.7080 (mmm) cc_final: 0.6715 (mmm) REVERT: H 114 MET cc_start: 0.6825 (tmm) cc_final: 0.6395 (tmm) REVERT: H 488 MET cc_start: 0.7972 (mmp) cc_final: 0.7649 (mmt) REVERT: H 514 MET cc_start: 0.8224 (ttm) cc_final: 0.7801 (ttm) REVERT: H 517 THR cc_start: 0.9469 (m) cc_final: 0.9164 (p) REVERT: I 114 MET cc_start: 0.6963 (tmm) cc_final: 0.6538 (tmm) REVERT: I 488 MET cc_start: 0.8598 (mmt) cc_final: 0.8181 (mmt) REVERT: J 25 ASP cc_start: 0.7751 (m-30) cc_final: 0.7538 (m-30) REVERT: J 203 TYR cc_start: 0.8421 (m-10) cc_final: 0.8161 (m-80) REVERT: K 114 MET cc_start: 0.6689 (tmm) cc_final: 0.6349 (tmm) REVERT: K 514 MET cc_start: 0.8240 (ttm) cc_final: 0.7999 (ttm) REVERT: K 517 THR cc_start: 0.9633 (m) cc_final: 0.9296 (p) REVERT: L 114 MET cc_start: 0.7104 (tmm) cc_final: 0.6687 (tmm) REVERT: L 307 MET cc_start: 0.8234 (pmm) cc_final: 0.7901 (pmm) REVERT: L 400 LEU cc_start: 0.9351 (tp) cc_final: 0.9111 (pp) REVERT: L 517 THR cc_start: 0.9411 (m) cc_final: 0.9024 (p) REVERT: M 22 VAL cc_start: 0.8658 (t) cc_final: 0.8279 (t) REVERT: M 267 MET cc_start: 0.6452 (mmm) cc_final: 0.5909 (mtp) REVERT: M 488 MET cc_start: 0.8328 (mmt) cc_final: 0.8126 (mmt) REVERT: N 22 VAL cc_start: 0.8651 (t) cc_final: 0.8416 (t) REVERT: N 111 MET cc_start: 0.6629 (tpp) cc_final: 0.6133 (tpp) REVERT: N 488 MET cc_start: 0.8300 (tpt) cc_final: 0.7699 (mmm) outliers start: 0 outliers final: 0 residues processed: 536 average time/residue: 0.4571 time to fit residues: 435.1129 Evaluate side-chains 427 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 4.9990 chunk 691 optimal weight: 10.0000 chunk 422 optimal weight: 0.8980 chunk 328 optimal weight: 5.9990 chunk 480 optimal weight: 0.7980 chunk 725 optimal weight: 3.9990 chunk 667 optimal weight: 0.9990 chunk 577 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 446 optimal weight: 6.9990 chunk 354 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 54894 Z= 0.217 Angle : 0.528 8.978 74214 Z= 0.284 Chirality : 0.041 0.151 9002 Planarity : 0.003 0.042 9632 Dihedral : 6.951 69.293 8218 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.10), residues: 7322 helix: 1.72 (0.08), residues: 4074 sheet: -0.02 (0.15), residues: 1050 loop : -0.08 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 401 PHE 0.012 0.001 PHE G 195 TYR 0.007 0.001 TYR K 203 ARG 0.004 0.000 ARG D 13 ********************** 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 522 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 522 time to evaluate : 4.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8489 (t) cc_final: 0.8239 (t) REVERT: A 114 MET cc_start: 0.6994 (tmm) cc_final: 0.6713 (tmm) REVERT: A 514 MET cc_start: 0.8408 (ttm) cc_final: 0.8092 (ttm) REVERT: A 517 THR cc_start: 0.9450 (m) cc_final: 0.9113 (p) REVERT: B 114 MET cc_start: 0.6883 (tmm) cc_final: 0.6536 (tmm) REVERT: B 488 MET cc_start: 0.8302 (mmt) cc_final: 0.7846 (mmp) REVERT: B 517 THR cc_start: 0.9400 (m) cc_final: 0.9020 (p) REVERT: C 114 MET cc_start: 0.6908 (tmm) cc_final: 0.6556 (tmm) REVERT: C 203 TYR cc_start: 0.8485 (m-10) cc_final: 0.8180 (m-80) REVERT: C 307 MET cc_start: 0.8536 (pmm) cc_final: 0.8224 (pmm) REVERT: C 389 MET cc_start: 0.8351 (mmp) cc_final: 0.8114 (mmp) REVERT: D 400 LEU cc_start: 0.9394 (tp) cc_final: 0.9190 (pp) REVERT: D 401 HIS cc_start: 0.8775 (m90) cc_final: 0.8569 (m90) REVERT: D 517 THR cc_start: 0.9568 (m) cc_final: 0.9180 (p) REVERT: E 307 MET cc_start: 0.8864 (pmm) cc_final: 0.8642 (pmm) REVERT: E 488 MET cc_start: 0.8180 (mmt) cc_final: 0.7599 (mmt) REVERT: G 22 VAL cc_start: 0.8832 (t) cc_final: 0.8415 (t) REVERT: G 111 MET cc_start: 0.7284 (mmm) cc_final: 0.7037 (mmm) REVERT: G 114 MET cc_start: 0.6627 (tmm) cc_final: 0.6385 (tmm) REVERT: G 288 MET cc_start: 0.9452 (ppp) cc_final: 0.9164 (ppp) REVERT: G 488 MET cc_start: 0.8505 (tpt) cc_final: 0.7779 (mmm) REVERT: H 114 MET cc_start: 0.6823 (tmm) cc_final: 0.6420 (tmm) REVERT: H 488 MET cc_start: 0.8035 (mmp) cc_final: 0.7594 (mmt) REVERT: H 517 THR cc_start: 0.9476 (m) cc_final: 0.9175 (p) REVERT: I 22 VAL cc_start: 0.8822 (t) cc_final: 0.8533 (t) REVERT: I 114 MET cc_start: 0.6894 (tmm) cc_final: 0.6456 (tmm) REVERT: I 488 MET cc_start: 0.8647 (mmt) cc_final: 0.8191 (mmt) REVERT: J 203 TYR cc_start: 0.8451 (m-10) cc_final: 0.8182 (m-80) REVERT: K 114 MET cc_start: 0.6692 (tmm) cc_final: 0.6379 (tmm) REVERT: K 514 MET cc_start: 0.8259 (ttm) cc_final: 0.7981 (ttm) REVERT: K 517 THR cc_start: 0.9638 (m) cc_final: 0.9300 (p) REVERT: L 69 MET cc_start: 0.8961 (mtp) cc_final: 0.8636 (mtt) REVERT: L 114 MET cc_start: 0.7156 (tmm) cc_final: 0.6693 (tmm) REVERT: L 307 MET cc_start: 0.8235 (pmm) cc_final: 0.7892 (pmm) REVERT: L 400 LEU cc_start: 0.9355 (tp) cc_final: 0.9130 (pp) REVERT: L 514 MET cc_start: 0.8734 (ttm) cc_final: 0.8489 (ttm) REVERT: L 517 THR cc_start: 0.9444 (m) cc_final: 0.9014 (p) REVERT: M 22 VAL cc_start: 0.8704 (t) cc_final: 0.8287 (t) REVERT: M 267 MET cc_start: 0.6483 (mmm) cc_final: 0.5921 (mtp) REVERT: M 400 LEU cc_start: 0.9279 (tt) cc_final: 0.9056 (pp) REVERT: N 22 VAL cc_start: 0.8660 (t) cc_final: 0.8406 (t) REVERT: N 111 MET cc_start: 0.6821 (tpp) cc_final: 0.6257 (tpp) REVERT: N 288 MET cc_start: 0.9368 (ppp) cc_final: 0.9135 (ppp) REVERT: N 488 MET cc_start: 0.8318 (tpt) cc_final: 0.7696 (mmm) outliers start: 0 outliers final: 0 residues processed: 522 average time/residue: 0.4603 time to fit residues: 424.8914 Evaluate side-chains 418 residues out of total 5670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 4.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 176 optimal weight: 30.0000 chunk 532 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 160 optimal weight: 0.0010 chunk 578 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 593 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.3392 ------------------------------------------------------------------------------- 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** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 457 ASN ** 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 = 0.3807 r_free = 0.3807 target = 0.087363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.055546 restraints weight = 234752.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057165 restraints weight = 143251.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.058258 restraints weight = 99745.167| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 54894 Z= 0.219 Angle : 0.534 10.901 74214 Z= 0.286 Chirality : 0.041 0.149 9002 Planarity : 0.003 0.037 9632 Dihedral : 6.910 69.440 8218 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.10), residues: 7322 helix: 1.70 (0.08), residues: 4088 sheet: -0.01 (0.15), residues: 1050 loop : -0.16 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 401 PHE 0.012 0.001 PHE G 195 TYR 0.007 0.001 TYR K 203 ARG 0.003 0.000 ARG M 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8594.38 seconds wall clock time: 154 minutes 50.00 seconds (9290.00 seconds total)