Starting phenix.real_space_refine on Mon Dec 11 03:04:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/12_2023/6vd7_21150.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/12_2023/6vd7_21150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/12_2023/6vd7_21150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/12_2023/6vd7_21150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/12_2023/6vd7_21150.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vd7_21150/12_2023/6vd7_21150.pdb" } resolution = 3.02 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= 0.008 sd= 0.694 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: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 11088 2.51 5 N 2513 2.21 5 O 2828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 329": "OD1" <-> "OD2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 329": "OD1" <-> "OD2" Residue "C GLU 343": "OE1" <-> "OE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 329": "OD1" <-> "OD2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "E PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 329": "OD1" <-> "OD2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 251": "NH1" <-> "NH2" Residue "F PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 329": "OD1" <-> "OD2" Residue "F GLU 343": "OE1" <-> "OE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 251": "NH1" <-> "NH2" Residue "G PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 329": "OD1" <-> "OD2" Residue "G GLU 343": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16506 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2358 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 8.64, per 1000 atoms: 0.52 Number of scatterers: 16506 At special positions: 0 Unit cell: (107, 109.14, 117.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 2828 8.00 N 2513 7.00 C 11088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 267 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 267 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 267 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 267 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 248 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.39 Conformation dependent library (CDL) restraints added in 2.9 seconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4060 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 69.4% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 33 through 61 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 84 removed outlier: 4.071A pdb=" N VAL A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 154 Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.621A pdb=" N LYS A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 298 Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 299 through 302 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.703A pdb=" N LEU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 removed outlier: 4.279A pdb=" N PHE A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 61 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 84 removed outlier: 4.071A pdb=" N VAL B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 154 Processing helix chain 'B' and resid 196 through 205 removed outlier: 3.622A pdb=" N LYS B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER B 241 " --> pdb=" O ILE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 298 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 299 through 302 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.702A pdb=" N LEU B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 4.278A pdb=" N PHE B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 61 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 84 removed outlier: 4.072A pdb=" N VAL C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU C 113 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 114 " --> pdb=" O PRO C 110 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 154 Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.621A pdb=" N LYS C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 298 Proline residue: C 291 - end of helix Processing helix chain 'C' and resid 299 through 302 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 328 through 341 removed outlier: 3.702A pdb=" N LEU C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 removed outlier: 4.278A pdb=" N PHE C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 61 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 84 removed outlier: 4.071A pdb=" N VAL D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU D 113 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 154 Processing helix chain 'D' and resid 196 through 205 removed outlier: 3.621A pdb=" N LYS D 205 " --> pdb=" O TYR D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 298 Proline residue: D 291 - end of helix Processing helix chain 'D' and resid 299 through 302 Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.703A pdb=" N LEU D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 357 removed outlier: 4.278A pdb=" N PHE D 349 " --> pdb=" O LYS D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 61 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 84 removed outlier: 4.071A pdb=" N VAL E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU E 113 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU E 114 " --> pdb=" O PRO E 110 " (cutoff:3.500A) Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 154 Processing helix chain 'E' and resid 196 through 205 removed outlier: 3.621A pdb=" N LYS E 205 " --> pdb=" O TYR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 241 removed outlier: 3.627A pdb=" N SER E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 298 Proline residue: E 291 - end of helix Processing helix chain 'E' and resid 299 through 302 Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 312 through 314 No H-bonds generated for 'chain 'E' and resid 312 through 314' Processing helix chain 'E' and resid 328 through 341 removed outlier: 3.703A pdb=" N LEU E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 357 removed outlier: 4.279A pdb=" N PHE E 349 " --> pdb=" O LYS E 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 61 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 84 removed outlier: 4.072A pdb=" N VAL F 80 " --> pdb=" O GLN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU F 113 " --> pdb=" O PHE F 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU F 114 " --> pdb=" O PRO F 110 " (cutoff:3.500A) Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 154 Processing helix chain 'F' and resid 196 through 205 removed outlier: 3.621A pdb=" N LYS F 205 " --> pdb=" O TYR F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER F 241 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 298 Proline residue: F 291 - end of helix Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 306 through 311 Processing helix chain 'F' and resid 312 through 314 No H-bonds generated for 'chain 'F' and resid 312 through 314' Processing helix chain 'F' and resid 328 through 341 removed outlier: 3.702A pdb=" N LEU F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 357 removed outlier: 4.279A pdb=" N PHE F 349 " --> pdb=" O LYS F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 61 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 84 removed outlier: 4.071A pdb=" N VAL G 80 " --> pdb=" O GLN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 108 Processing helix chain 'G' and resid 108 through 131 removed outlier: 3.671A pdb=" N LEU G 113 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 154 Processing helix chain 'G' and resid 196 through 205 removed outlier: 3.622A pdb=" N LYS G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 241 removed outlier: 3.628A pdb=" N SER G 241 " --> pdb=" O ILE G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 298 Proline residue: G 291 - end of helix Processing helix chain 'G' and resid 299 through 302 Processing helix chain 'G' and resid 306 through 311 Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 328 through 341 removed outlier: 3.702A pdb=" N LEU G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 357 removed outlier: 4.278A pdb=" N PHE G 349 " --> pdb=" O LYS G 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 1022 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.79 Time building geometry restraints manager: 6.87 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: 4815 1.34 - 1.46: 3531 1.46 - 1.57: 8496 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 16940 Sorted by residual: bond pdb=" CB THR C 59 " pdb=" CG2 THR C 59 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.73e+00 bond pdb=" CB THR E 59 " pdb=" CG2 THR E 59 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.72e+00 bond pdb=" CB THR B 59 " pdb=" CG2 THR B 59 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.72e+00 bond pdb=" CB THR A 59 " pdb=" CG2 THR A 59 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" CB THR F 59 " pdb=" CG2 THR F 59 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 ... (remaining 16935 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.05: 497 107.05 - 113.78: 9724 113.78 - 120.52: 7064 120.52 - 127.25: 5675 127.25 - 133.98: 182 Bond angle restraints: 23142 Sorted by residual: angle pdb=" N VAL A 299 " pdb=" CA VAL A 299 " pdb=" C VAL A 299 " ideal model delta sigma weight residual 108.88 116.03 -7.15 2.16e+00 2.14e-01 1.10e+01 angle pdb=" N VAL D 299 " pdb=" CA VAL D 299 " pdb=" C VAL D 299 " ideal model delta sigma weight residual 108.88 116.03 -7.15 2.16e+00 2.14e-01 1.10e+01 angle pdb=" N VAL B 299 " pdb=" CA VAL B 299 " pdb=" C VAL B 299 " ideal model delta sigma weight residual 108.88 116.03 -7.15 2.16e+00 2.14e-01 1.09e+01 angle pdb=" N VAL G 299 " pdb=" CA VAL G 299 " pdb=" C VAL G 299 " ideal model delta sigma weight residual 108.88 116.02 -7.14 2.16e+00 2.14e-01 1.09e+01 angle pdb=" N VAL C 299 " pdb=" CA VAL C 299 " pdb=" C VAL C 299 " ideal model delta sigma weight residual 108.88 116.02 -7.14 2.16e+00 2.14e-01 1.09e+01 ... (remaining 23137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.11: 8325 12.11 - 24.22: 1083 24.22 - 36.32: 525 36.32 - 48.43: 42 48.43 - 60.54: 28 Dihedral angle restraints: 10003 sinusoidal: 3759 harmonic: 6244 Sorted by residual: dihedral pdb=" CA GLU B 22 " pdb=" C GLU B 22 " pdb=" N SER B 23 " pdb=" CA SER B 23 " ideal model delta harmonic sigma weight residual 180.00 149.34 30.66 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA GLU E 22 " pdb=" C GLU E 22 " pdb=" N SER E 23 " pdb=" CA SER E 23 " ideal model delta harmonic sigma weight residual 180.00 149.37 30.63 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA GLU A 22 " pdb=" C GLU A 22 " pdb=" N SER A 23 " pdb=" CA SER A 23 " ideal model delta harmonic sigma weight residual 180.00 149.40 30.60 0 5.00e+00 4.00e-02 3.75e+01 ... (remaining 10000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1556 0.032 - 0.065: 870 0.065 - 0.097: 205 0.097 - 0.129: 141 0.129 - 0.161: 21 Chirality restraints: 2793 Sorted by residual: chirality pdb=" CB THR C 59 " pdb=" CA THR C 59 " pdb=" OG1 THR C 59 " pdb=" CG2 THR C 59 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB THR E 59 " pdb=" CA THR E 59 " pdb=" OG1 THR E 59 " pdb=" CG2 THR E 59 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CB THR B 59 " pdb=" CA THR B 59 " pdb=" OG1 THR B 59 " pdb=" CG2 THR B 59 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 2790 not shown) Planarity restraints: 2793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 33 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C ALA G 33 " -0.068 2.00e-02 2.50e+03 pdb=" O ALA G 33 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL G 34 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 33 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C ALA F 33 " 0.068 2.00e-02 2.50e+03 pdb=" O ALA F 33 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL F 34 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 33 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C ALA C 33 " -0.068 2.00e-02 2.50e+03 pdb=" O ALA C 33 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL C 34 " 0.023 2.00e-02 2.50e+03 ... (remaining 2790 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4842 2.81 - 3.33: 15941 3.33 - 3.85: 25709 3.85 - 4.38: 29155 4.38 - 4.90: 51521 Nonbonded interactions: 127168 Sorted by model distance: nonbonded pdb=" O TYR C 201 " pdb=" OG1 THR C 204 " model vdw 2.284 2.440 nonbonded pdb=" O TYR A 201 " pdb=" OG1 THR A 204 " model vdw 2.284 2.440 nonbonded pdb=" O TYR D 201 " pdb=" OG1 THR D 204 " model vdw 2.284 2.440 nonbonded pdb=" O TYR E 201 " pdb=" OG1 THR E 204 " model vdw 2.284 2.440 nonbonded pdb=" O TYR G 201 " pdb=" OG1 THR G 204 " model vdw 2.284 2.440 ... (remaining 127163 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' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.640 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 42.740 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.008 0.049 16940 Z= 0.493 Angle : 0.765 7.149 23142 Z= 0.413 Chirality : 0.045 0.161 2793 Planarity : 0.004 0.040 2793 Dihedral : 13.380 60.537 5901 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 0.78 % Allowed : 6.17 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.17), residues: 2037 helix: -0.17 (0.14), residues: 1260 sheet: -0.97 (0.48), residues: 84 loop : -4.80 (0.18), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 85 HIS 0.002 0.001 HIS F 330 PHE 0.017 0.002 PHE F 240 TYR 0.018 0.002 TYR E 25 ARG 0.002 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 315 time to evaluate : 1.797 Fit side-chains outliers start: 14 outliers final: 1 residues processed: 315 average time/residue: 0.2848 time to fit residues: 132.9701 Evaluate side-chains 222 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 2.045 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1511 time to fit residues: 2.9737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 184 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 207 ASN B 266 GLN C 63 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN C 207 ASN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN D 266 GLN D 282 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 ASN G 266 GLN G 282 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16940 Z= 0.178 Angle : 0.613 7.441 23142 Z= 0.317 Chirality : 0.040 0.184 2793 Planarity : 0.004 0.025 2793 Dihedral : 5.289 27.736 2240 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 2.17 % Allowed : 12.28 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 2037 helix: 1.27 (0.15), residues: 1274 sheet: None (None), residues: 0 loop : -4.03 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 74 HIS 0.003 0.001 HIS D 106 PHE 0.013 0.001 PHE G 54 TYR 0.013 0.001 TYR C 25 ARG 0.003 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 245 time to evaluate : 2.154 Fit side-chains outliers start: 39 outliers final: 20 residues processed: 269 average time/residue: 0.2395 time to fit residues: 102.1347 Evaluate side-chains 247 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 227 time to evaluate : 1.992 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1507 time to fit residues: 8.3499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN B 106 HIS ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16940 Z= 0.333 Angle : 0.661 7.935 23142 Z= 0.340 Chirality : 0.043 0.191 2793 Planarity : 0.004 0.028 2793 Dihedral : 5.361 29.030 2240 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.95 % Allowed : 16.62 % Favored : 81.43 % 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: -0.42 (0.20), residues: 2037 helix: 1.52 (0.15), residues: 1288 sheet: -0.16 (0.54), residues: 84 loop : -4.19 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 104 HIS 0.003 0.001 HIS E 106 PHE 0.014 0.002 PHE D 126 TYR 0.017 0.002 TYR F 25 ARG 0.003 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 241 time to evaluate : 1.805 Fit side-chains outliers start: 35 outliers final: 31 residues processed: 271 average time/residue: 0.2486 time to fit residues: 105.9628 Evaluate side-chains 252 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 221 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1767 time to fit residues: 12.1914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 88 optimal weight: 0.0000 chunk 124 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 175 optimal weight: 0.0670 chunk 52 optimal weight: 4.9990 overall best weight: 1.6128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16940 Z= 0.201 Angle : 0.597 6.922 23142 Z= 0.307 Chirality : 0.041 0.209 2793 Planarity : 0.004 0.026 2793 Dihedral : 5.102 26.978 2240 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 1.22 % Allowed : 19.12 % Favored : 79.66 % 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: 0.07 (0.20), residues: 2037 helix: 1.86 (0.15), residues: 1295 sheet: -0.31 (0.50), residues: 84 loop : -3.93 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 104 HIS 0.002 0.001 HIS E 106 PHE 0.009 0.001 PHE D 126 TYR 0.014 0.001 TYR B 327 ARG 0.002 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 1.990 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 20 residues processed: 304 average time/residue: 0.2426 time to fit residues: 116.5067 Evaluate side-chains 253 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 233 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1446 time to fit residues: 7.9683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 176 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16940 Z= 0.197 Angle : 0.590 6.996 23142 Z= 0.303 Chirality : 0.040 0.210 2793 Planarity : 0.004 0.027 2793 Dihedral : 4.924 26.494 2240 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.45 % Allowed : 21.57 % Favored : 76.99 % 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: 0.29 (0.21), residues: 2037 helix: 2.03 (0.15), residues: 1295 sheet: -0.45 (0.49), residues: 84 loop : -3.80 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 104 HIS 0.002 0.001 HIS B 330 PHE 0.009 0.001 PHE G 83 TYR 0.013 0.001 TYR D 25 ARG 0.002 0.000 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 257 time to evaluate : 1.937 Fit side-chains outliers start: 26 outliers final: 21 residues processed: 276 average time/residue: 0.2485 time to fit residues: 108.0332 Evaluate side-chains 270 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 249 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1666 time to fit residues: 8.7725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN C 106 HIS ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16940 Z= 0.409 Angle : 0.711 8.533 23142 Z= 0.365 Chirality : 0.045 0.232 2793 Planarity : 0.004 0.033 2793 Dihedral : 5.344 28.850 2240 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.95 % Allowed : 21.29 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 2037 helix: 1.78 (0.15), residues: 1288 sheet: -0.21 (0.52), residues: 84 loop : -3.80 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 104 HIS 0.003 0.001 HIS G 106 PHE 0.018 0.002 PHE E 126 TYR 0.021 0.002 TYR B 25 ARG 0.002 0.000 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 271 time to evaluate : 2.060 Fit side-chains outliers start: 35 outliers final: 24 residues processed: 291 average time/residue: 0.2510 time to fit residues: 114.2038 Evaluate side-chains 269 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 1.946 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1603 time to fit residues: 9.5687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 165 optimal weight: 0.0970 chunk 109 optimal weight: 1.9990 chunk 195 optimal weight: 0.0970 chunk 122 optimal weight: 0.4980 chunk 119 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN A 330 HIS ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 HIS ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS G 151 ASN G 282 ASN G 330 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16940 Z= 0.175 Angle : 0.596 7.540 23142 Z= 0.303 Chirality : 0.040 0.201 2793 Planarity : 0.004 0.030 2793 Dihedral : 4.870 24.886 2240 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.78 % Allowed : 22.35 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 2037 helix: 2.15 (0.15), residues: 1302 sheet: -0.45 (0.48), residues: 84 loop : -3.69 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.002 0.001 HIS D 106 PHE 0.009 0.001 PHE G 83 TYR 0.010 0.001 TYR F 79 ARG 0.003 0.000 ARG E 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 290 time to evaluate : 1.884 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 299 average time/residue: 0.2546 time to fit residues: 118.6090 Evaluate side-chains 257 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 250 time to evaluate : 1.933 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1798 time to fit residues: 4.7372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN D 330 HIS ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16940 Z= 0.179 Angle : 0.590 7.763 23142 Z= 0.302 Chirality : 0.041 0.213 2793 Planarity : 0.004 0.033 2793 Dihedral : 4.697 25.762 2240 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.33 % Allowed : 24.12 % Favored : 75.54 % 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: 0.56 (0.21), residues: 2037 helix: 2.28 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -3.48 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.002 0.001 HIS F 330 PHE 0.008 0.001 PHE G 83 TYR 0.015 0.001 TYR A 111 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 266 time to evaluate : 1.829 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 272 average time/residue: 0.2639 time to fit residues: 111.3537 Evaluate side-chains 256 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 251 time to evaluate : 1.767 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1450 time to fit residues: 3.7966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 172 optimal weight: 0.0980 chunk 181 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16940 Z= 0.288 Angle : 0.650 7.580 23142 Z= 0.334 Chirality : 0.043 0.218 2793 Planarity : 0.004 0.035 2793 Dihedral : 4.929 28.188 2240 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.78 % Allowed : 24.07 % Favored : 75.15 % 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: 0.42 (0.20), residues: 2037 helix: 2.18 (0.15), residues: 1288 sheet: None (None), residues: 0 loop : -3.43 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 104 HIS 0.004 0.001 HIS F 330 PHE 0.013 0.001 PHE E 126 TYR 0.018 0.001 TYR D 25 ARG 0.004 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 254 time to evaluate : 1.891 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 262 average time/residue: 0.2629 time to fit residues: 107.3713 Evaluate side-chains 249 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 239 time to evaluate : 2.072 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1623 time to fit residues: 5.6378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 2.9990 chunk 117 optimal weight: 0.0670 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 0.4980 chunk 127 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16940 Z= 0.174 Angle : 0.593 7.431 23142 Z= 0.303 Chirality : 0.040 0.219 2793 Planarity : 0.004 0.035 2793 Dihedral : 4.667 24.746 2240 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.33 % Allowed : 24.12 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 2037 helix: 2.31 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -3.44 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.003 0.001 HIS G 330 PHE 0.007 0.001 PHE B 83 TYR 0.010 0.001 TYR A 25 ARG 0.002 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 279 time to evaluate : 2.013 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 283 average time/residue: 0.2584 time to fit residues: 114.7617 Evaluate side-chains 260 residues out of total 1904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 257 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1458 time to fit residues: 3.3680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 165 optimal weight: 0.1980 chunk 20 optimal weight: 0.0170 chunk 29 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS D 63 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106110 restraints weight = 27163.917| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.39 r_work: 0.3214 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16940 Z= 0.171 Angle : 0.587 6.860 23142 Z= 0.301 Chirality : 0.040 0.219 2793 Planarity : 0.004 0.036 2793 Dihedral : 4.513 24.700 2240 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.44 % Allowed : 24.51 % Favored : 75.04 % 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: 0.68 (0.21), residues: 2037 helix: 2.33 (0.15), residues: 1309 sheet: None (None), residues: 0 loop : -3.39 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.002 0.001 HIS A 330 PHE 0.008 0.001 PHE E 83 TYR 0.008 0.001 TYR C 79 ARG 0.002 0.000 ARG G 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3151.14 seconds wall clock time: 58 minutes 23.71 seconds (3503.71 seconds total)