Starting phenix.real_space_refine on Sat Mar 16 18:48:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/03_2024/6cno_7539.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/03_2024/6cno_7539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/03_2024/6cno_7539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/03_2024/6cno_7539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/03_2024/6cno_7539.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cno_7539/03_2024/6cno_7539.pdb" } resolution = 4.7 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= 0.001 sd= 0.027 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 Ca 12 9.91 5 S 108 5.16 5 C 9884 2.51 5 N 2744 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 14": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 352": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 352": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ARG 331": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15428 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2781 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "F" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "G" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1073 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 59 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.29, per 1000 atoms: 0.54 Number of scatterers: 15428 At special positions: 0 Unit cell: (116.39, 116.39, 106.09, 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) Ca 12 19.99 S 108 16.00 O 2680 8.00 N 2744 7.00 C 9884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.30 Conformation dependent library (CDL) restraints added in 2.9 seconds 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 75.9% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 9 through 49 removed outlier: 3.600A pdb=" N ARG A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.543A pdb=" N LEU A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 Processing helix chain 'A' and resid 147 through 155 removed outlier: 4.539A pdb=" N LEU A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR A 161 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 162 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 170 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 205 through 227 removed outlier: 3.630A pdb=" N GLY A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALA A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 249 removed outlier: 4.346A pdb=" N TRP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 261 through 289 removed outlier: 3.507A pdb=" N VAL A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 331 removed outlier: 3.935A pdb=" N HIS A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 367 removed outlier: 4.221A pdb=" N ARG A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 386 Processing helix chain 'B' and resid 9 through 49 removed outlier: 3.599A pdb=" N ARG B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.542A pdb=" N LEU B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 115 Processing helix chain 'B' and resid 147 through 155 removed outlier: 4.539A pdb=" N LEU B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR B 161 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 162 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 205 through 227 removed outlier: 3.631A pdb=" N GLY B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALA B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 249 removed outlier: 4.345A pdb=" N TRP B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Proline residue: B 245 - end of helix Processing helix chain 'B' and resid 261 through 289 removed outlier: 3.506A pdb=" N VAL B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 331 removed outlier: 3.934A pdb=" N HIS B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 367 removed outlier: 4.219A pdb=" N ARG B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 386 Processing helix chain 'C' and resid 9 through 49 removed outlier: 3.600A pdb=" N ARG C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 91 removed outlier: 3.542A pdb=" N LEU C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 115 Processing helix chain 'C' and resid 147 through 155 removed outlier: 4.540A pdb=" N LEU C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR C 161 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 162 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 170 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 205 through 227 removed outlier: 3.631A pdb=" N GLY C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA C 220 " --> pdb=" O TRP C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 249 removed outlier: 4.346A pdb=" N TRP C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Proline residue: C 245 - end of helix Processing helix chain 'C' and resid 261 through 289 removed outlier: 3.506A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 331 removed outlier: 3.934A pdb=" N HIS C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 367 removed outlier: 4.219A pdb=" N ARG C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 343 " --> pdb=" O ARG C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 386 Processing helix chain 'D' and resid 9 through 49 removed outlier: 3.600A pdb=" N ARG D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 3.543A pdb=" N LEU D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 91 " --> pdb=" O PHE D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 115 Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.540A pdb=" N LEU D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 removed outlier: 3.935A pdb=" N LEU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR D 161 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 162 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 205 through 227 removed outlier: 3.631A pdb=" N GLY D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA D 220 " --> pdb=" O TRP D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 removed outlier: 4.346A pdb=" N TRP D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Proline residue: D 245 - end of helix Processing helix chain 'D' and resid 261 through 289 removed outlier: 3.507A pdb=" N VAL D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 331 removed outlier: 3.934A pdb=" N HIS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 309 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 367 removed outlier: 4.220A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 386 Processing helix chain 'E' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 39 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 65 through 74 removed outlier: 3.531A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 92 Processing helix chain 'E' and resid 102 through 110 removed outlier: 3.672A pdb=" N THR E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'F' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 44 through 55 Processing helix chain 'F' and resid 65 through 74 removed outlier: 3.530A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 92 Processing helix chain 'F' and resid 102 through 110 removed outlier: 3.672A pdb=" N THR F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'G' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 39 Processing helix chain 'G' and resid 44 through 55 Processing helix chain 'G' and resid 65 through 74 removed outlier: 3.531A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG G 74 " --> pdb=" O THR G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 92 Processing helix chain 'G' and resid 102 through 110 removed outlier: 3.672A pdb=" N THR G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 138 through 147 Processing helix chain 'H' and resid 6 through 20 removed outlier: 3.680A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 39 Processing helix chain 'H' and resid 44 through 55 Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.530A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 92 Processing helix chain 'H' and resid 102 through 110 removed outlier: 3.671A pdb=" N THR H 110 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 138 through 147 Processing sheet with id= A, first strand: chain 'E' and resid 26 through 27 Processing sheet with id= B, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= C, first strand: chain 'F' and resid 26 through 27 Processing sheet with id= D, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= E, first strand: chain 'G' and resid 26 through 27 Processing sheet with id= F, first strand: chain 'G' and resid 99 through 101 Processing sheet with id= G, first strand: chain 'H' and resid 26 through 27 Processing sheet with id= H, first strand: chain 'H' and resid 99 through 101 1076 hydrogen bonds defined for protein. 3204 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: 4.40 Time building geometry restraints manager: 6.74 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: 4963 1.34 - 1.46: 2695 1.46 - 1.57: 7850 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 15696 Sorted by residual: bond pdb=" CG1 ILE C 244 " pdb=" CD1 ILE C 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" CG1 ILE D 244 " pdb=" CD1 ILE D 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" CG1 ILE B 244 " pdb=" CD1 ILE B 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" CG1 ILE A 244 " pdb=" CD1 ILE A 244 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" CA ALA D 220 " pdb=" CB ALA D 220 " ideal model delta sigma weight residual 1.528 1.506 0.022 1.59e-02 3.96e+03 1.97e+00 ... (remaining 15691 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.11: 212 105.11 - 112.37: 8213 112.37 - 119.62: 5282 119.62 - 126.87: 7316 126.87 - 134.13: 209 Bond angle restraints: 21232 Sorted by residual: angle pdb=" C ASP F 64 " pdb=" N PHE F 65 " pdb=" CA PHE F 65 " ideal model delta sigma weight residual 120.58 127.19 -6.61 1.32e+00 5.74e-01 2.50e+01 angle pdb=" C ASP E 64 " pdb=" N PHE E 65 " pdb=" CA PHE E 65 " ideal model delta sigma weight residual 120.58 127.19 -6.61 1.32e+00 5.74e-01 2.50e+01 angle pdb=" C ASP G 64 " pdb=" N PHE G 65 " pdb=" CA PHE G 65 " ideal model delta sigma weight residual 120.58 127.16 -6.58 1.32e+00 5.74e-01 2.49e+01 angle pdb=" C ASP H 64 " pdb=" N PHE H 65 " pdb=" CA PHE H 65 " ideal model delta sigma weight residual 120.58 127.13 -6.55 1.32e+00 5.74e-01 2.46e+01 angle pdb=" C THR E 5 " pdb=" N GLU E 6 " pdb=" CA GLU E 6 " ideal model delta sigma weight residual 120.28 124.98 -4.70 1.34e+00 5.57e-01 1.23e+01 ... (remaining 21227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.69: 8093 9.69 - 19.37: 991 19.37 - 29.06: 124 29.06 - 38.74: 96 38.74 - 48.43: 16 Dihedral angle restraints: 9320 sinusoidal: 3512 harmonic: 5808 Sorted by residual: dihedral pdb=" CA GLU F 114 " pdb=" C GLU F 114 " pdb=" N LYS F 115 " pdb=" CA LYS F 115 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLU E 114 " pdb=" C GLU E 114 " pdb=" N LYS E 115 " pdb=" CA LYS E 115 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU G 114 " pdb=" C GLU G 114 " pdb=" N LYS G 115 " pdb=" CA LYS G 115 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 9317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1592 0.044 - 0.088: 694 0.088 - 0.131: 159 0.131 - 0.175: 27 0.175 - 0.219: 8 Chirality restraints: 2480 Sorted by residual: chirality pdb=" CB ILE D 377 " pdb=" CA ILE D 377 " pdb=" CG1 ILE D 377 " pdb=" CG2 ILE D 377 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE B 377 " pdb=" CA ILE B 377 " pdb=" CG1 ILE B 377 " pdb=" CG2 ILE B 377 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE C 377 " pdb=" CA ILE C 377 " pdb=" CG1 ILE C 377 " pdb=" CG2 ILE C 377 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2477 not shown) Planarity restraints: 2660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 189 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.43e+00 pdb=" C ARG C 189 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG C 189 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE C 190 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 189 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C ARG A 189 " 0.044 2.00e-02 2.50e+03 pdb=" O ARG A 189 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE A 190 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 369 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C VAL C 369 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL C 369 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP C 370 " 0.014 2.00e-02 2.50e+03 ... (remaining 2657 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 251 2.53 - 3.12: 11797 3.12 - 3.71: 24852 3.71 - 4.31: 32150 4.31 - 4.90: 51120 Nonbonded interactions: 120170 Sorted by model distance: nonbonded pdb=" OD1 ASP E 93 " pdb=" OD1 ASN E 97 " model vdw 1.936 3.040 nonbonded pdb=" OD1 ASP H 93 " pdb=" OD1 ASN H 97 " model vdw 1.937 3.040 nonbonded pdb=" OD1 ASP G 93 " pdb=" OD1 ASN G 97 " model vdw 1.937 3.040 nonbonded pdb=" OD1 ASP F 93 " pdb=" OD1 ASN F 97 " model vdw 1.937 3.040 nonbonded pdb=" OD2 ASP F 24 " pdb="CA CA F 201 " model vdw 1.939 2.510 ... (remaining 120165 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' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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: 1.740 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: 0.020 Extract box with map and model: 6.600 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 42.580 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.006 0.066 15696 Z= 0.402 Angle : 1.029 9.714 21232 Z= 0.595 Chirality : 0.049 0.219 2480 Planarity : 0.006 0.054 2660 Dihedral : 9.243 48.428 5560 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.26 % Allowed : 0.53 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.15), residues: 2000 helix: -1.61 (0.10), residues: 1528 sheet: None (None), residues: 0 loop : -1.67 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 221 HIS 0.011 0.003 HIS A 80 PHE 0.017 0.003 PHE G 92 TYR 0.022 0.003 TYR D 307 ARG 0.007 0.001 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.273 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: A 18 LEU cc_start: 0.9531 (mt) cc_final: 0.9146 (pp) REVERT: A 22 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8731 (mt-10) REVERT: A 82 LYS cc_start: 0.9382 (mmtt) cc_final: 0.9067 (mmmm) REVERT: A 87 PHE cc_start: 0.9171 (t80) cc_final: 0.8950 (t80) REVERT: A 176 ASN cc_start: 0.9284 (t0) cc_final: 0.8677 (t0) REVERT: A 179 TYR cc_start: 0.9090 (m-80) cc_final: 0.8337 (m-10) REVERT: A 186 ASN cc_start: 0.9406 (t0) cc_final: 0.9183 (t0) REVERT: A 194 PHE cc_start: 0.8762 (t80) cc_final: 0.8096 (t80) REVERT: A 200 MET cc_start: 0.9434 (ttm) cc_final: 0.8812 (tpp) REVERT: A 201 ASN cc_start: 0.9348 (m-40) cc_final: 0.9076 (p0) REVERT: A 261 MET cc_start: 0.8292 (tmm) cc_final: 0.7964 (mmt) REVERT: A 273 MET cc_start: 0.9087 (mtm) cc_final: 0.8842 (ptt) REVERT: A 278 THR cc_start: 0.9168 (m) cc_final: 0.8927 (p) REVERT: A 288 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8381 (tmtt) REVERT: A 292 ASN cc_start: 0.9399 (t0) cc_final: 0.9183 (t0) REVERT: A 303 MET cc_start: 0.8791 (mmm) cc_final: 0.8500 (mmm) REVERT: A 309 LYS cc_start: 0.9557 (ttpt) cc_final: 0.9184 (ttmm) REVERT: A 312 LYS cc_start: 0.9498 (mttm) cc_final: 0.9137 (tmtt) REVERT: A 321 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8504 (tp30) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.1851 time to fit residues: 31.3143 Evaluate side-chains 90 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.327 Evaluate side-chains 66 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 LEU cc_start: 0.9065 (tp) cc_final: 0.8852 (tp) REVERT: E 9 ILE cc_start: 0.9586 (mt) cc_final: 0.9346 (mt) REVERT: E 16 PHE cc_start: 0.9531 (t80) cc_final: 0.9146 (t80) REVERT: E 48 LEU cc_start: 0.9689 (mt) cc_final: 0.9402 (tt) REVERT: E 54 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8136 (mt-10) REVERT: E 68 PHE cc_start: 0.9296 (t80) cc_final: 0.9017 (t80) REVERT: E 74 ARG cc_start: 0.8871 (mtm110) cc_final: 0.8536 (mtm-85) REVERT: E 75 LYS cc_start: 0.9330 (mmtt) cc_final: 0.8782 (mmmt) REVERT: E 90 ARG cc_start: 0.9351 (ttm110) cc_final: 0.9100 (ttm110) REVERT: E 92 PHE cc_start: 0.8926 (m-10) cc_final: 0.8331 (m-80) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1835 time to fit residues: 12.9349 Evaluate side-chains 54 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 80 optimal weight: 0.0980 chunk 156 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 0.0010 chunk 116 optimal weight: 0.1980 chunk 181 optimal weight: 0.9980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.877 15696 Z= 2.105 Angle : 0.787 22.969 21232 Z= 0.394 Chirality : 0.036 0.118 2480 Planarity : 0.004 0.044 2660 Dihedral : 5.311 24.960 2168 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2000 helix: 0.47 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -1.28 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP D 242 HIS 0.004 0.001 HIS B 328 PHE 0.025 0.002 PHE H 89 TYR 0.009 0.001 TYR E 138 ARG 0.007 0.001 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9581 (mt) cc_final: 0.9180 (pp) REVERT: A 19 LEU cc_start: 0.9529 (mt) cc_final: 0.9234 (mt) REVERT: A 82 LYS cc_start: 0.9382 (mmtt) cc_final: 0.8992 (mmmt) REVERT: A 91 ASN cc_start: 0.8876 (m-40) cc_final: 0.8227 (m110) REVERT: A 111 GLU cc_start: 0.8854 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 115 CYS cc_start: 0.9356 (t) cc_final: 0.8707 (p) REVERT: A 198 LEU cc_start: 0.9266 (mt) cc_final: 0.8756 (mt) REVERT: A 201 ASN cc_start: 0.9364 (m-40) cc_final: 0.8994 (p0) REVERT: A 207 LEU cc_start: 0.8970 (mt) cc_final: 0.8557 (pp) REVERT: A 261 MET cc_start: 0.8566 (tmm) cc_final: 0.8179 (mmt) REVERT: A 264 LYS cc_start: 0.7952 (mttt) cc_final: 0.7652 (tttt) REVERT: A 270 THR cc_start: 0.8688 (p) cc_final: 0.8326 (p) REVERT: A 273 MET cc_start: 0.9124 (mtm) cc_final: 0.8724 (ptp) REVERT: A 292 ASN cc_start: 0.9429 (t0) cc_final: 0.8930 (t0) REVERT: A 303 MET cc_start: 0.8807 (mmm) cc_final: 0.8498 (mmp) REVERT: A 309 LYS cc_start: 0.9478 (ttpt) cc_final: 0.9059 (ttmm) REVERT: A 310 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9060 (mt-10) REVERT: A 321 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8397 (tp30) REVERT: A 324 MET cc_start: 0.9437 (tpt) cc_final: 0.9132 (tpt) REVERT: A 343 LYS cc_start: 0.9578 (mttt) cc_final: 0.9099 (mptt) REVERT: A 359 ARG cc_start: 0.8371 (ttt180) cc_final: 0.7798 (ttp80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1839 time to fit residues: 26.4507 Evaluate side-chains 90 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.332 Evaluate side-chains 66 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 GLN cc_start: 0.9289 (mp10) cc_final: 0.9063 (mp10) REVERT: H 13 LYS cc_start: 0.9585 (tppt) cc_final: 0.9246 (mmmm) REVERT: H 16 PHE cc_start: 0.9514 (t80) cc_final: 0.9066 (t80) REVERT: H 36 MET cc_start: 0.8976 (tpt) cc_final: 0.8459 (tpt) REVERT: H 48 LEU cc_start: 0.9736 (mt) cc_final: 0.9425 (tt) REVERT: H 72 MET cc_start: 0.8965 (tpp) cc_final: 0.8684 (tpp) REVERT: H 74 ARG cc_start: 0.8824 (mtm110) cc_final: 0.8576 (mtm-85) REVERT: H 75 LYS cc_start: 0.9146 (mmtt) cc_final: 0.8542 (mttt) REVERT: H 84 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8060 (mm-30) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2033 time to fit residues: 14.3727 Evaluate side-chains 53 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 196 optimal weight: 6.9990 chunk 162 optimal weight: 0.0170 chunk 180 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.034 1.954 15696 Z= 2.036 Angle : 0.945 19.709 21232 Z= 0.475 Chirality : 0.045 0.412 2480 Planarity : 0.006 0.055 2660 Dihedral : 5.600 23.874 2168 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.26 % Allowed : 4.22 % Favored : 95.51 % 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: 0.18 (0.19), residues: 2000 helix: 0.69 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -1.58 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.006 TRP D 242 HIS 0.007 0.002 HIS C 80 PHE 0.027 0.003 PHE D 144 TYR 0.039 0.003 TYR C 253 ARG 0.015 0.001 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9459 (mt) cc_final: 0.8999 (mm) REVERT: A 22 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8580 (mt-10) REVERT: A 82 LYS cc_start: 0.9385 (mmtt) cc_final: 0.9018 (mmmt) REVERT: A 91 ASN cc_start: 0.8746 (m-40) cc_final: 0.8212 (m-40) REVERT: A 176 ASN cc_start: 0.9442 (t0) cc_final: 0.9201 (t0) REVERT: A 179 TYR cc_start: 0.8630 (m-80) cc_final: 0.8301 (m-10) REVERT: A 198 LEU cc_start: 0.9222 (mt) cc_final: 0.8782 (mt) REVERT: A 207 LEU cc_start: 0.8930 (mt) cc_final: 0.8526 (pp) REVERT: A 261 MET cc_start: 0.8519 (tmm) cc_final: 0.8144 (mmt) REVERT: A 270 THR cc_start: 0.8735 (p) cc_final: 0.8359 (p) REVERT: A 273 MET cc_start: 0.9082 (mtm) cc_final: 0.8709 (ptp) REVERT: A 303 MET cc_start: 0.8859 (mmm) cc_final: 0.8600 (mmm) REVERT: A 309 LYS cc_start: 0.9479 (ttpt) cc_final: 0.9092 (ttmm) REVERT: A 310 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9060 (mt-10) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1457 time to fit residues: 18.7943 Evaluate side-chains 88 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.327 Evaluate side-chains 65 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: E 4 LEU cc_start: 0.8919 (tp) cc_final: 0.8163 (tp) REVERT: E 12 PHE cc_start: 0.9435 (m-80) cc_final: 0.9115 (m-80) REVERT: E 16 PHE cc_start: 0.9613 (t80) cc_final: 0.9145 (t80) REVERT: E 48 LEU cc_start: 0.9731 (mt) cc_final: 0.9402 (tt) REVERT: E 51 MET cc_start: 0.8704 (tpp) cc_final: 0.8133 (tpp) REVERT: E 54 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8458 (mt-10) REVERT: E 64 ASP cc_start: 0.9336 (p0) cc_final: 0.9121 (p0) REVERT: E 75 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8463 (mttt) REVERT: E 84 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8185 (mm-30) REVERT: E 137 ASN cc_start: 0.9024 (m-40) cc_final: 0.8726 (m-40) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1863 time to fit residues: 12.8946 Evaluate side-chains 52 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 0.3980 chunk 122 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 193 optimal weight: 0.0970 chunk 95 optimal weight: 0.0270 chunk 173 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 300 ASN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.922 15696 Z= 2.010 Angle : 0.774 18.947 21232 Z= 0.400 Chirality : 0.042 0.400 2480 Planarity : 0.006 0.075 2660 Dihedral : 5.442 30.977 2168 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.53 % Allowed : 2.37 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.36 (0.19), residues: 2000 helix: 0.78 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -1.26 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP B 242 HIS 0.005 0.001 HIS C 328 PHE 0.027 0.004 PHE B 144 TYR 0.021 0.002 TYR A 253 ARG 0.018 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9557 (mt) cc_final: 0.9174 (pp) REVERT: A 22 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8748 (mt-10) REVERT: A 82 LYS cc_start: 0.9469 (mmtt) cc_final: 0.9069 (mmmt) REVERT: A 91 ASN cc_start: 0.8296 (m-40) cc_final: 0.7922 (m-40) REVERT: A 198 LEU cc_start: 0.9223 (mt) cc_final: 0.8673 (mt) REVERT: A 261 MET cc_start: 0.8520 (tmm) cc_final: 0.8115 (mmt) REVERT: A 273 MET cc_start: 0.9176 (mtm) cc_final: 0.8788 (ptp) REVERT: A 295 GLU cc_start: 0.9170 (mp0) cc_final: 0.8968 (mp0) REVERT: A 296 LYS cc_start: 0.9188 (mptt) cc_final: 0.8982 (mptt) REVERT: A 303 MET cc_start: 0.8904 (mmm) cc_final: 0.8523 (mmm) REVERT: A 309 LYS cc_start: 0.9481 (ttpt) cc_final: 0.9122 (ttmm) REVERT: A 310 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8985 (mt-10) REVERT: A 320 GLN cc_start: 0.8805 (pp30) cc_final: 0.8357 (pp30) outliers start: 2 outliers final: 1 residues processed: 109 average time/residue: 0.1623 time to fit residues: 20.6266 Evaluate side-chains 90 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.326 Evaluate side-chains 58 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 4 LEU cc_start: 0.8930 (tp) cc_final: 0.8183 (tp) REVERT: E 12 PHE cc_start: 0.9390 (m-80) cc_final: 0.8990 (m-80) REVERT: E 16 PHE cc_start: 0.9587 (t80) cc_final: 0.8977 (t80) REVERT: E 48 LEU cc_start: 0.9712 (mt) cc_final: 0.9453 (tt) REVERT: E 53 ASN cc_start: 0.9365 (m110) cc_final: 0.8712 (m110) REVERT: E 75 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8373 (mttt) REVERT: E 77 LYS cc_start: 0.8676 (tppt) cc_final: 0.8350 (tptt) REVERT: E 83 GLU cc_start: 0.8876 (pp20) cc_final: 0.8669 (pp20) REVERT: E 92 PHE cc_start: 0.8650 (m-10) cc_final: 0.8141 (m-80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1793 time to fit residues: 11.1136 Evaluate side-chains 52 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 164 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.919 15696 Z= 2.019 Angle : 0.868 19.656 21232 Z= 0.452 Chirality : 0.043 0.363 2480 Planarity : 0.008 0.104 2660 Dihedral : 5.401 30.796 2168 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.23 (0.18), residues: 2000 helix: 0.67 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -1.28 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP C 242 HIS 0.017 0.003 HIS D 340 PHE 0.027 0.003 PHE A 144 TYR 0.024 0.003 TYR A 253 ARG 0.028 0.002 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.332 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: A 18 LEU cc_start: 0.9592 (mt) cc_final: 0.9212 (pp) REVERT: A 22 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8684 (mt-10) REVERT: A 40 MET cc_start: 0.7791 (tmm) cc_final: 0.7585 (tmm) REVERT: A 82 LYS cc_start: 0.9487 (mmtt) cc_final: 0.9090 (mmmt) REVERT: A 90 ASP cc_start: 0.8367 (t70) cc_final: 0.8151 (t0) REVERT: A 91 ASN cc_start: 0.8282 (m-40) cc_final: 0.7870 (m-40) REVERT: A 117 LEU cc_start: 0.9364 (mt) cc_final: 0.8500 (mt) REVERT: A 176 ASN cc_start: 0.9339 (t0) cc_final: 0.8332 (t0) REVERT: A 179 TYR cc_start: 0.8460 (m-80) cc_final: 0.7959 (m-80) REVERT: A 198 LEU cc_start: 0.9204 (mt) cc_final: 0.8746 (mt) REVERT: A 261 MET cc_start: 0.8562 (tmm) cc_final: 0.8139 (mmt) REVERT: A 270 THR cc_start: 0.8914 (p) cc_final: 0.8538 (p) REVERT: A 273 MET cc_start: 0.9212 (mtm) cc_final: 0.8886 (ptp) REVERT: A 296 LYS cc_start: 0.9159 (mptt) cc_final: 0.8831 (mptt) REVERT: A 303 MET cc_start: 0.8842 (mmm) cc_final: 0.8498 (mmm) REVERT: A 309 LYS cc_start: 0.9482 (ttpt) cc_final: 0.9146 (ttmm) REVERT: A 310 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9006 (mt-10) REVERT: A 320 GLN cc_start: 0.8836 (pp30) cc_final: 0.8394 (pp30) REVERT: A 326 TYR cc_start: 0.8661 (t80) cc_final: 0.8402 (t80) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1860 time to fit residues: 23.0779 Evaluate side-chains 88 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.356 Evaluate side-chains 56 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.9004 (tp) cc_final: 0.8273 (tp) REVERT: H 12 PHE cc_start: 0.9426 (m-80) cc_final: 0.9053 (m-80) REVERT: H 16 PHE cc_start: 0.9588 (t80) cc_final: 0.8974 (t80) REVERT: H 48 LEU cc_start: 0.9712 (mt) cc_final: 0.9441 (tt) REVERT: H 75 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8403 (mttt) REVERT: H 84 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7823 (mm-30) REVERT: H 87 GLU cc_start: 0.9226 (tt0) cc_final: 0.8993 (pp20) REVERT: H 89 PHE cc_start: 0.9468 (t80) cc_final: 0.8915 (t80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1711 time to fit residues: 10.3035 Evaluate side-chains 49 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 193 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.919 15696 Z= 2.018 Angle : 0.880 19.559 21232 Z= 0.446 Chirality : 0.044 0.353 2480 Planarity : 0.008 0.095 2660 Dihedral : 5.476 31.164 2168 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.31 (0.18), residues: 2000 helix: 0.75 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.29 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP D 242 HIS 0.010 0.002 HIS B 80 PHE 0.029 0.004 PHE A 301 TYR 0.025 0.003 TYR C 161 ARG 0.013 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9587 (mt) cc_final: 0.9362 (mt) REVERT: A 19 LEU cc_start: 0.9573 (mt) cc_final: 0.9298 (mm) REVERT: A 22 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8691 (mt-10) REVERT: A 82 LYS cc_start: 0.9476 (mmtt) cc_final: 0.9049 (mmmt) REVERT: A 90 ASP cc_start: 0.8435 (t70) cc_final: 0.8211 (t0) REVERT: A 91 ASN cc_start: 0.8285 (m-40) cc_final: 0.7955 (m-40) REVERT: A 175 LEU cc_start: 0.9521 (mt) cc_final: 0.9202 (pp) REVERT: A 198 LEU cc_start: 0.9230 (mt) cc_final: 0.8756 (mt) REVERT: A 251 ILE cc_start: 0.6296 (mt) cc_final: 0.6078 (mt) REVERT: A 261 MET cc_start: 0.8561 (tmm) cc_final: 0.8141 (mmt) REVERT: A 270 THR cc_start: 0.8945 (p) cc_final: 0.8611 (p) REVERT: A 273 MET cc_start: 0.9232 (mtm) cc_final: 0.8873 (ptp) REVERT: A 296 LYS cc_start: 0.9171 (mttt) cc_final: 0.8893 (mptt) REVERT: A 303 MET cc_start: 0.8897 (mmm) cc_final: 0.8474 (mmm) REVERT: A 309 LYS cc_start: 0.9465 (ttpt) cc_final: 0.9120 (ttmm) REVERT: A 310 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9007 (mt-10) REVERT: A 320 GLN cc_start: 0.8806 (pp30) cc_final: 0.8429 (pp30) REVERT: A 321 GLU cc_start: 0.9094 (tp30) cc_final: 0.8775 (tp30) REVERT: A 326 TYR cc_start: 0.8706 (t80) cc_final: 0.8400 (t80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1670 time to fit residues: 20.5461 Evaluate side-chains 90 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.344 Evaluate side-chains 55 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 4 LEU cc_start: 0.9017 (tp) cc_final: 0.8291 (tp) REVERT: G 12 PHE cc_start: 0.9420 (m-80) cc_final: 0.9003 (m-80) REVERT: G 16 PHE cc_start: 0.9597 (t80) cc_final: 0.9008 (t80) REVERT: G 48 LEU cc_start: 0.9718 (mt) cc_final: 0.9441 (tt) REVERT: G 75 LYS cc_start: 0.9034 (mmtt) cc_final: 0.8333 (mttt) REVERT: G 76 MET cc_start: 0.8501 (tmm) cc_final: 0.8258 (tmm) REVERT: G 77 LYS cc_start: 0.8755 (tppt) cc_final: 0.8326 (tptt) REVERT: G 83 GLU cc_start: 0.9155 (pm20) cc_final: 0.8566 (pm20) REVERT: G 84 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8396 (mm-30) REVERT: G 87 GLU cc_start: 0.9163 (tt0) cc_final: 0.8946 (pp20) REVERT: G 92 PHE cc_start: 0.9085 (m-80) cc_final: 0.8620 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1698 time to fit residues: 10.0717 Evaluate side-chains 49 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 162 optimal weight: 0.0000 chunk 108 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 120 optimal weight: 0.0020 chunk 117 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.917 15696 Z= 2.016 Angle : 0.918 19.682 21232 Z= 0.465 Chirality : 0.043 0.346 2480 Planarity : 0.006 0.054 2660 Dihedral : 5.355 30.489 2168 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.13 (0.18), residues: 2000 helix: 0.61 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 242 HIS 0.012 0.002 HIS D 80 PHE 0.027 0.004 PHE B 144 TYR 0.018 0.003 TYR A 179 ARG 0.014 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9579 (mt) cc_final: 0.9191 (pp) REVERT: A 22 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8737 (mt-10) REVERT: A 40 MET cc_start: 0.7832 (tmm) cc_final: 0.7625 (tmm) REVERT: A 82 LYS cc_start: 0.9479 (mmtt) cc_final: 0.9073 (mmmt) REVERT: A 90 ASP cc_start: 0.8396 (t70) cc_final: 0.8161 (t0) REVERT: A 91 ASN cc_start: 0.8237 (m-40) cc_final: 0.7916 (m-40) REVERT: A 175 LEU cc_start: 0.9501 (mt) cc_final: 0.9181 (pp) REVERT: A 176 ASN cc_start: 0.9360 (t0) cc_final: 0.8125 (t0) REVERT: A 179 TYR cc_start: 0.8224 (m-80) cc_final: 0.7709 (m-80) REVERT: A 198 LEU cc_start: 0.9212 (mt) cc_final: 0.8775 (mt) REVERT: A 207 LEU cc_start: 0.8575 (mt) cc_final: 0.8122 (pp) REVERT: A 251 ILE cc_start: 0.6301 (mt) cc_final: 0.6072 (mt) REVERT: A 261 MET cc_start: 0.8566 (tmm) cc_final: 0.8195 (mmt) REVERT: A 273 MET cc_start: 0.9241 (mtm) cc_final: 0.8874 (ptp) REVERT: A 296 LYS cc_start: 0.9172 (mttt) cc_final: 0.8892 (mptt) REVERT: A 303 MET cc_start: 0.8823 (mmm) cc_final: 0.8505 (mmm) REVERT: A 309 LYS cc_start: 0.9461 (ttpt) cc_final: 0.9147 (ttmm) REVERT: A 310 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8988 (mt-10) REVERT: A 313 GLU cc_start: 0.9000 (pp20) cc_final: 0.8604 (pp20) REVERT: A 320 GLN cc_start: 0.8814 (pp30) cc_final: 0.8408 (pp30) REVERT: A 321 GLU cc_start: 0.9068 (tp30) cc_final: 0.8718 (tp30) REVERT: A 326 TYR cc_start: 0.8695 (t80) cc_final: 0.8375 (t80) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1504 time to fit residues: 18.6378 Evaluate side-chains 94 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.320 Evaluate side-chains 53 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8973 (tp) cc_final: 0.8246 (tp) REVERT: H 12 PHE cc_start: 0.9402 (m-80) cc_final: 0.8999 (m-80) REVERT: H 16 PHE cc_start: 0.9568 (t80) cc_final: 0.8979 (t80) REVERT: H 48 LEU cc_start: 0.9711 (mt) cc_final: 0.9450 (tt) REVERT: H 53 ASN cc_start: 0.9339 (m110) cc_final: 0.8686 (m110) REVERT: H 75 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8361 (mttt) REVERT: H 77 LYS cc_start: 0.8797 (tppt) cc_final: 0.8568 (tptt) REVERT: H 83 GLU cc_start: 0.9136 (pm20) cc_final: 0.8606 (pm20) REVERT: H 84 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8375 (mm-30) REVERT: H 87 GLU cc_start: 0.9219 (tt0) cc_final: 0.8970 (pp20) REVERT: H 92 PHE cc_start: 0.9035 (m-80) cc_final: 0.8539 (m-80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1671 time to fit residues: 9.5355 Evaluate side-chains 51 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 8.9990 chunk 76 optimal weight: 0.1980 chunk 115 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 chunk 122 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 151 optimal weight: 0.0670 chunk 175 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.6657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.917 15696 Z= 2.016 Angle : 0.918 19.682 21232 Z= 0.465 Chirality : 0.043 0.346 2480 Planarity : 0.006 0.054 2660 Dihedral : 5.355 30.489 2168 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 30.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.13 (0.18), residues: 2000 helix: 0.61 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 242 HIS 0.012 0.002 HIS B 80 PHE 0.027 0.004 PHE D 144 TYR 0.018 0.003 TYR B 179 ARG 0.014 0.001 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9575 (mt) cc_final: 0.9188 (pp) REVERT: A 22 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8749 (mt-10) REVERT: A 40 MET cc_start: 0.7842 (tmm) cc_final: 0.7618 (tmm) REVERT: A 82 LYS cc_start: 0.9481 (mmtt) cc_final: 0.9071 (mmmt) REVERT: A 90 ASP cc_start: 0.8412 (t70) cc_final: 0.8161 (t0) REVERT: A 91 ASN cc_start: 0.8249 (m-40) cc_final: 0.7914 (m-40) REVERT: A 176 ASN cc_start: 0.9351 (t0) cc_final: 0.8122 (t0) REVERT: A 179 TYR cc_start: 0.8224 (m-80) cc_final: 0.7720 (m-80) REVERT: A 198 LEU cc_start: 0.9206 (mt) cc_final: 0.8775 (mt) REVERT: A 207 LEU cc_start: 0.8578 (mt) cc_final: 0.8124 (pp) REVERT: A 251 ILE cc_start: 0.6298 (mt) cc_final: 0.6071 (mt) REVERT: A 261 MET cc_start: 0.8584 (tmm) cc_final: 0.8195 (mmt) REVERT: A 273 MET cc_start: 0.9241 (mtm) cc_final: 0.8874 (ptp) REVERT: A 303 MET cc_start: 0.8863 (mmm) cc_final: 0.8505 (mmm) REVERT: A 309 LYS cc_start: 0.9457 (ttpt) cc_final: 0.9147 (ttmm) REVERT: A 310 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8987 (mt-10) REVERT: A 313 GLU cc_start: 0.8994 (pp20) cc_final: 0.8603 (pp20) REVERT: A 320 GLN cc_start: 0.8813 (pp30) cc_final: 0.8408 (pp30) REVERT: A 321 GLU cc_start: 0.9068 (tp30) cc_final: 0.8719 (tp30) REVERT: A 326 TYR cc_start: 0.8693 (t80) cc_final: 0.8376 (t80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1449 time to fit residues: 17.5981 Evaluate side-chains 94 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.338 Evaluate side-chains 53 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8974 (tp) cc_final: 0.8247 (tp) REVERT: H 12 PHE cc_start: 0.9402 (m-80) cc_final: 0.9000 (m-80) REVERT: H 16 PHE cc_start: 0.9556 (t80) cc_final: 0.8981 (t80) REVERT: H 48 LEU cc_start: 0.9702 (mt) cc_final: 0.9450 (tt) REVERT: H 53 ASN cc_start: 0.9345 (m110) cc_final: 0.8684 (m110) REVERT: H 75 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8360 (mttt) REVERT: H 83 GLU cc_start: 0.9141 (pm20) cc_final: 0.8606 (pm20) REVERT: H 84 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8375 (mm-30) REVERT: H 87 GLU cc_start: 0.9214 (tt0) cc_final: 0.8969 (pp20) REVERT: H 92 PHE cc_start: 0.9035 (m-80) cc_final: 0.8539 (m-80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1692 time to fit residues: 9.6401 Evaluate side-chains 51 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 179 optimal weight: 0.3980 chunk 108 optimal weight: 9.9990 chunk 78 optimal weight: 0.0980 chunk 141 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 162 optimal weight: 0.0060 chunk 169 optimal weight: 0.0010 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.917 15696 Z= 2.016 Angle : 0.918 19.682 21232 Z= 0.465 Chirality : 0.043 0.346 2480 Planarity : 0.006 0.054 2660 Dihedral : 5.355 30.489 2168 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 31.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.13 (0.18), residues: 2000 helix: 0.61 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 242 HIS 0.012 0.002 HIS C 80 PHE 0.027 0.004 PHE B 144 TYR 0.018 0.003 TYR A 179 ARG 0.014 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9575 (mt) cc_final: 0.9188 (pp) REVERT: A 22 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8749 (mt-10) REVERT: A 40 MET cc_start: 0.7841 (tmm) cc_final: 0.7617 (tmm) REVERT: A 82 LYS cc_start: 0.9481 (mmtt) cc_final: 0.9071 (mmmt) REVERT: A 90 ASP cc_start: 0.8412 (t70) cc_final: 0.8162 (t0) REVERT: A 91 ASN cc_start: 0.8249 (m-40) cc_final: 0.7915 (m-40) REVERT: A 176 ASN cc_start: 0.9351 (t0) cc_final: 0.8123 (t0) REVERT: A 179 TYR cc_start: 0.8224 (m-80) cc_final: 0.7720 (m-80) REVERT: A 198 LEU cc_start: 0.9206 (mt) cc_final: 0.8775 (mt) REVERT: A 207 LEU cc_start: 0.8578 (mt) cc_final: 0.8123 (pp) REVERT: A 251 ILE cc_start: 0.6299 (mt) cc_final: 0.6072 (mt) REVERT: A 261 MET cc_start: 0.8584 (tmm) cc_final: 0.8195 (mmt) REVERT: A 273 MET cc_start: 0.9241 (mtm) cc_final: 0.8875 (ptp) REVERT: A 303 MET cc_start: 0.8863 (mmm) cc_final: 0.8505 (mmm) REVERT: A 309 LYS cc_start: 0.9456 (ttpt) cc_final: 0.9148 (ttmm) REVERT: A 310 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8989 (mt-10) REVERT: A 313 GLU cc_start: 0.8994 (pp20) cc_final: 0.8615 (pp20) REVERT: A 320 GLN cc_start: 0.8813 (pp30) cc_final: 0.8405 (pp30) REVERT: A 321 GLU cc_start: 0.9067 (tp30) cc_final: 0.8740 (tp30) REVERT: A 326 TYR cc_start: 0.8693 (t80) cc_final: 0.8377 (t80) REVERT: A 343 LYS cc_start: 0.9588 (mttt) cc_final: 0.9124 (mptt) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1509 time to fit residues: 18.2925 Evaluate side-chains 94 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.354 Evaluate side-chains 53 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8974 (tp) cc_final: 0.8247 (tp) REVERT: H 12 PHE cc_start: 0.9403 (m-80) cc_final: 0.9000 (m-80) REVERT: H 16 PHE cc_start: 0.9560 (t80) cc_final: 0.8981 (t80) REVERT: H 48 LEU cc_start: 0.9702 (mt) cc_final: 0.9450 (tt) REVERT: H 53 ASN cc_start: 0.9345 (m110) cc_final: 0.8684 (m110) REVERT: H 75 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8360 (mttt) REVERT: H 83 GLU cc_start: 0.9140 (pm20) cc_final: 0.8606 (pm20) REVERT: H 84 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8375 (mm-30) REVERT: H 87 GLU cc_start: 0.9215 (tt0) cc_final: 0.8969 (pp20) REVERT: H 92 PHE cc_start: 0.9034 (m-80) cc_final: 0.8539 (m-80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1622 time to fit residues: 9.2592 Evaluate side-chains 51 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 199 optimal weight: 50.0000 chunk 183 optimal weight: 0.5980 chunk 158 optimal weight: 7.9990 chunk 16 optimal weight: 0.0870 chunk 122 optimal weight: 0.0020 chunk 97 optimal weight: 0.0980 chunk 126 optimal weight: 2.9990 chunk 169 optimal weight: 0.3980 overall best weight: 0.2366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.917 15696 Z= 2.016 Angle : 0.918 19.682 21232 Z= 0.465 Chirality : 0.043 0.346 2480 Planarity : 0.006 0.054 2660 Dihedral : 5.355 30.489 2168 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 31.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.13 (0.18), residues: 2000 helix: 0.61 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 242 HIS 0.012 0.002 HIS B 80 PHE 0.027 0.004 PHE B 144 TYR 0.018 0.003 TYR D 179 ARG 0.014 0.001 ARG C 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.9575 (mt) cc_final: 0.9188 (pp) REVERT: A 22 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8749 (mt-10) REVERT: A 40 MET cc_start: 0.7841 (tmm) cc_final: 0.7617 (tmm) REVERT: A 82 LYS cc_start: 0.9481 (mmtt) cc_final: 0.9071 (mmmt) REVERT: A 90 ASP cc_start: 0.8412 (t70) cc_final: 0.8162 (t0) REVERT: A 91 ASN cc_start: 0.8249 (m-40) cc_final: 0.7915 (m-40) REVERT: A 176 ASN cc_start: 0.9351 (t0) cc_final: 0.8123 (t0) REVERT: A 179 TYR cc_start: 0.8224 (m-80) cc_final: 0.7720 (m-80) REVERT: A 198 LEU cc_start: 0.9206 (mt) cc_final: 0.8775 (mt) REVERT: A 207 LEU cc_start: 0.8578 (mt) cc_final: 0.8123 (pp) REVERT: A 251 ILE cc_start: 0.6299 (mt) cc_final: 0.6072 (mt) REVERT: A 261 MET cc_start: 0.8584 (tmm) cc_final: 0.8195 (mmt) REVERT: A 273 MET cc_start: 0.9241 (mtm) cc_final: 0.8875 (ptp) REVERT: A 303 MET cc_start: 0.8863 (mmm) cc_final: 0.8505 (mmm) REVERT: A 309 LYS cc_start: 0.9456 (ttpt) cc_final: 0.9148 (ttmm) REVERT: A 310 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8989 (mt-10) REVERT: A 313 GLU cc_start: 0.8994 (pp20) cc_final: 0.8615 (pp20) REVERT: A 320 GLN cc_start: 0.8813 (pp30) cc_final: 0.8405 (pp30) REVERT: A 321 GLU cc_start: 0.9067 (tp30) cc_final: 0.8740 (tp30) REVERT: A 326 TYR cc_start: 0.8693 (t80) cc_final: 0.8377 (t80) REVERT: A 343 LYS cc_start: 0.9588 (mttt) cc_final: 0.9124 (mptt) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1437 time to fit residues: 17.3988 Evaluate side-chains 94 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.303 Evaluate side-chains 53 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8974 (tp) cc_final: 0.8247 (tp) REVERT: H 12 PHE cc_start: 0.9403 (m-80) cc_final: 0.9000 (m-80) REVERT: H 16 PHE cc_start: 0.9560 (t80) cc_final: 0.8981 (t80) REVERT: H 48 LEU cc_start: 0.9702 (mt) cc_final: 0.9450 (tt) REVERT: H 53 ASN cc_start: 0.9345 (m110) cc_final: 0.8684 (m110) REVERT: H 75 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8360 (mttt) REVERT: H 83 GLU cc_start: 0.9140 (pm20) cc_final: 0.8606 (pm20) REVERT: H 84 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8375 (mm-30) REVERT: H 87 GLU cc_start: 0.9215 (tt0) cc_final: 0.8969 (pp20) REVERT: H 92 PHE cc_start: 0.9034 (m-80) cc_final: 0.8539 (m-80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1645 time to fit residues: 9.3760 Evaluate side-chains 51 residues out of total 125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 0.0370 chunk 158 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 163 optimal weight: 7.9990 chunk 20 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 139 optimal weight: 0.0040 chunk 9 optimal weight: 3.9990 overall best weight: 0.2870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.098020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.073191 restraints weight = 12183.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.075271 restraints weight = 6982.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.076549 restraints weight = 4897.726| |-----------------------------------------------------------------------------| r_work (final): 0.3373 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.050594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.040723 restraints weight = 6227.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.042349 restraints weight = 3896.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.043496 restraints weight = 2747.207| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.917 15696 Z= 2.016 Angle : 0.918 19.682 21232 Z= 0.465 Chirality : 0.043 0.346 2480 Planarity : 0.006 0.054 2660 Dihedral : 5.355 30.489 2168 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 31.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.13 (0.18), residues: 2000 helix: 0.61 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.32 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 242 HIS 0.012 0.002 HIS C 80 PHE 0.027 0.004 PHE C 144 TYR 0.018 0.003 TYR A 179 ARG 0.014 0.001 ARG C 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2485.93 seconds wall clock time: 46 minutes 14.84 seconds (2774.84 seconds total)