Starting phenix.real_space_refine on Fri Sep 27 14:13:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/09_2024/7k0r_22610.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/09_2024/7k0r_22610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/09_2024/7k0r_22610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/09_2024/7k0r_22610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/09_2024/7k0r_22610.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0r_22610/09_2024/7k0r_22610.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 60 5.16 5 C 10290 2.51 5 N 2580 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "E" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "F" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Time building chain proxies: 9.28, per 1000 atoms: 0.58 Number of scatterers: 16038 At special positions: 0 Unit cell: (107.63, 106.485, 124.805, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 12 15.00 O 3096 8.00 N 2580 7.00 C 10290 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 - 3.00 Amino acid : True - 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: 4.21 Conformation dependent library (CDL) restraints added in 2.2 seconds 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3876 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 27.0% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.516A pdb=" N GLU A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 251 through 262 removed outlier: 3.515A pdb=" N GLU B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 251 through 262 removed outlier: 3.515A pdb=" N GLU C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 208 through 217 Processing helix chain 'D' and resid 218 through 226 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.515A pdb=" N GLU D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 69 through 76 Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 208 through 217 Processing helix chain 'E' and resid 218 through 226 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 251 through 262 removed outlier: 3.515A pdb=" N GLU E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 69 through 76 Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 130 through 138 Processing helix chain 'F' and resid 208 through 217 Processing helix chain 'F' and resid 218 through 226 Processing helix chain 'F' and resid 232 through 237 Processing helix chain 'F' and resid 251 through 262 removed outlier: 3.515A pdb=" N GLU F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.676A pdb=" N VAL A 32 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.900A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP A 125 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.900A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP A 125 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS A 181 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100 removed outlier: 7.861A pdb=" N THR A 99 " --> pdb=" O ILE A 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 264 through 267 removed outlier: 4.794A pdb=" N ILE A 281 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N CYS A 291 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP A 283 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER A 289 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 323 removed outlier: 7.553A pdb=" N SER A 329 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET A 331 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 342 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP A 333 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.675A pdb=" N VAL B 32 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 100 removed outlier: 7.861A pdb=" N THR B 99 " --> pdb=" O ILE B 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 267 removed outlier: 4.793A pdb=" N ILE B 281 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N CYS B 291 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP B 283 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER B 289 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 316 through 323 removed outlier: 7.553A pdb=" N SER B 329 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET B 331 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 342 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP B 333 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.676A pdb=" N VAL C 32 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC3, first strand: chain 'C' and resid 99 through 100 removed outlier: 7.862A pdb=" N THR C 99 " --> pdb=" O ILE C 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 160 through 163 Processing sheet with id=AC5, first strand: chain 'C' and resid 264 through 267 removed outlier: 4.794A pdb=" N ILE C 281 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N CYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 316 through 323 removed outlier: 7.554A pdb=" N SER C 329 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET C 331 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE C 342 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP C 333 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.677A pdb=" N VAL D 32 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS D 181 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'D' and resid 99 through 100 removed outlier: 7.861A pdb=" N THR D 99 " --> pdb=" O ILE D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 160 through 163 Processing sheet with id=AD4, first strand: chain 'D' and resid 264 through 267 removed outlier: 4.794A pdb=" N ILE D 281 " --> pdb=" O CYS D 291 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N CYS D 291 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP D 283 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER D 289 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 316 through 323 removed outlier: 7.553A pdb=" N SER D 329 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET D 331 " --> pdb=" O PHE D 342 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 342 " --> pdb=" O MET D 331 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP D 333 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.676A pdb=" N VAL E 32 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS E 181 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE1, first strand: chain 'E' and resid 99 through 100 removed outlier: 7.861A pdb=" N THR E 99 " --> pdb=" O ILE E 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 160 through 163 Processing sheet with id=AE3, first strand: chain 'E' and resid 264 through 267 removed outlier: 4.794A pdb=" N ILE E 281 " --> pdb=" O CYS E 291 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N CYS E 291 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP E 283 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER E 289 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 316 through 323 removed outlier: 7.554A pdb=" N SER E 329 " --> pdb=" O PRO E 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET E 331 " --> pdb=" O PHE E 342 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE E 342 " --> pdb=" O MET E 331 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP E 333 " --> pdb=" O GLU E 340 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.676A pdb=" N VAL F 32 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS F 181 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'F' and resid 99 through 100 removed outlier: 7.860A pdb=" N THR F 99 " --> pdb=" O ILE F 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 160 through 163 Processing sheet with id=AF2, first strand: chain 'F' and resid 264 through 267 removed outlier: 4.794A pdb=" N ILE F 281 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N CYS F 291 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP F 283 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER F 289 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 316 through 323 removed outlier: 7.554A pdb=" N SER F 329 " --> pdb=" O PRO F 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET F 331 " --> pdb=" O PHE F 342 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE F 342 " --> pdb=" O MET F 331 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP F 333 " --> pdb=" O GLU F 340 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1710 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: 5.74 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5106 1.33 - 1.45: 2192 1.45 - 1.57: 8980 1.57 - 1.68: 6 1.68 - 1.80: 90 Bond restraints: 16374 Sorted by residual: bond pdb=" O3 PO4 D 402 " pdb=" P PO4 D 402 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O3 PO4 F 402 " pdb=" P PO4 F 402 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.75e+00 bond pdb=" O3 PO4 A 402 " pdb=" P PO4 A 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 16369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 21279 1.67 - 3.34: 925 3.34 - 5.01: 113 5.01 - 6.68: 18 6.68 - 8.35: 3 Bond angle restraints: 22338 Sorted by residual: angle pdb=" O1P U5P B 401 " pdb=" P U5P B 401 " pdb=" O2P U5P B 401 " ideal model delta sigma weight residual 119.60 111.25 8.35 3.00e+00 1.11e-01 7.75e+00 angle pdb=" O1P U5P C 401 " pdb=" P U5P C 401 " pdb=" O2P U5P C 401 " ideal model delta sigma weight residual 119.60 111.29 8.31 3.00e+00 1.11e-01 7.68e+00 angle pdb=" O1P U5P A 401 " pdb=" P U5P A 401 " pdb=" O2P U5P A 401 " ideal model delta sigma weight residual 119.60 111.29 8.31 3.00e+00 1.11e-01 7.68e+00 angle pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " pdb=" CG TYR A 231 " ideal model delta sigma weight residual 113.90 109.32 4.58 1.80e+00 3.09e-01 6.46e+00 angle pdb=" CA TYR B 231 " pdb=" CB TYR B 231 " pdb=" CG TYR B 231 " ideal model delta sigma weight residual 113.90 109.35 4.55 1.80e+00 3.09e-01 6.38e+00 ... (remaining 22333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 8934 17.06 - 34.12: 576 34.12 - 51.19: 114 51.19 - 68.25: 72 68.25 - 85.31: 30 Dihedral angle restraints: 9726 sinusoidal: 3720 harmonic: 6006 Sorted by residual: dihedral pdb=" CA PHE A 177 " pdb=" C PHE A 177 " pdb=" N ASN A 178 " pdb=" CA ASN A 178 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PHE E 177 " pdb=" C PHE E 177 " pdb=" N ASN E 178 " pdb=" CA ASN E 178 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PHE D 177 " pdb=" C PHE D 177 " pdb=" N ASN D 178 " pdb=" CA ASN D 178 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 9723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1261 0.032 - 0.063: 726 0.063 - 0.095: 398 0.095 - 0.127: 168 0.127 - 0.158: 69 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CA ILE A 80 " pdb=" N ILE A 80 " pdb=" C ILE A 80 " pdb=" CB ILE A 80 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CB ILE B 28 " pdb=" CA ILE B 28 " pdb=" CG1 ILE B 28 " pdb=" CG2 ILE B 28 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE F 169 " pdb=" N ILE F 169 " pdb=" C ILE F 169 " pdb=" CB ILE F 169 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 2619 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 59 " -0.010 2.00e-02 2.50e+03 1.05e-02 2.78e+00 pdb=" CG TRP C 59 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP C 59 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 59 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 59 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 59 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 59 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 59 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 59 " -0.010 2.00e-02 2.50e+03 1.05e-02 2.73e+00 pdb=" CG TRP B 59 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 59 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 59 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 59 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 59 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 59 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 59 " 0.010 2.00e-02 2.50e+03 1.04e-02 2.72e+00 pdb=" CG TRP D 59 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP D 59 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 59 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 59 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 59 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 59 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 59 " 0.001 2.00e-02 2.50e+03 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 355 2.68 - 3.23: 15668 3.23 - 3.79: 26538 3.79 - 4.34: 35240 4.34 - 4.90: 58713 Nonbonded interactions: 136514 Sorted by model distance: nonbonded pdb=" NE2 HIS A 235 " pdb=" O1 PO4 A 402 " model vdw 2.122 3.120 nonbonded pdb=" NE2 HIS E 235 " pdb=" O3 PO4 E 402 " model vdw 2.122 3.120 nonbonded pdb=" NE2 HIS D 235 " pdb=" O3 PO4 D 402 " model vdw 2.122 3.120 nonbonded pdb=" NE2 HIS B 235 " pdb=" O1 PO4 B 402 " model vdw 2.122 3.120 nonbonded pdb=" NE2 HIS C 235 " pdb=" O1 PO4 C 402 " model vdw 2.122 3.120 ... (remaining 136509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.420 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.010 0.065 16374 Z= 0.639 Angle : 0.786 8.353 22338 Z= 0.434 Chirality : 0.054 0.158 2622 Planarity : 0.004 0.030 2856 Dihedral : 14.417 85.311 5850 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.05 % Allowed : 4.21 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2058 helix: -1.17 (0.19), residues: 534 sheet: -0.50 (0.26), residues: 336 loop : -0.46 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 59 HIS 0.008 0.002 HIS E 96 PHE 0.026 0.003 PHE D 177 TYR 0.025 0.003 TYR B 231 ARG 0.005 0.001 ARG F 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.858 Fit side-chains REVERT: A 68 PRO cc_start: 0.8223 (Cg_exo) cc_final: 0.7961 (Cg_endo) REVERT: B 245 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7645 (tp40) REVERT: B 331 MET cc_start: 0.6147 (mmm) cc_final: 0.5912 (tpt) REVERT: C 219 MET cc_start: 0.8251 (ttp) cc_final: 0.7654 (ttm) REVERT: E 245 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7183 (tp40) outliers start: 18 outliers final: 2 residues processed: 137 average time/residue: 0.2750 time to fit residues: 57.6472 Evaluate side-chains 60 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 245 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.3980 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 ASN F 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16374 Z= 0.167 Angle : 0.508 4.470 22338 Z= 0.278 Chirality : 0.045 0.173 2622 Planarity : 0.003 0.034 2856 Dihedral : 9.685 59.858 2330 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.99 % Allowed : 7.37 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2058 helix: 0.29 (0.22), residues: 534 sheet: 0.90 (0.26), residues: 318 loop : -0.15 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 333 HIS 0.004 0.001 HIS D 235 PHE 0.013 0.001 PHE A 330 TYR 0.019 0.001 TYR B 238 ARG 0.005 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.864 Fit side-chains REVERT: A 68 PRO cc_start: 0.7997 (Cg_exo) cc_final: 0.7742 (Cg_endo) REVERT: B 105 MET cc_start: 0.8141 (mmm) cc_final: 0.7886 (tpt) REVERT: B 331 MET cc_start: 0.6581 (mmm) cc_final: 0.6206 (tpp) REVERT: C 105 MET cc_start: 0.8402 (tpt) cc_final: 0.7833 (tpt) REVERT: C 219 MET cc_start: 0.7890 (ttp) cc_final: 0.7494 (ttm) REVERT: D 307 ILE cc_start: 0.5641 (tt) cc_final: 0.5348 (tt) outliers start: 17 outliers final: 11 residues processed: 91 average time/residue: 0.2836 time to fit residues: 41.6763 Evaluate side-chains 65 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 2 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN B 29 ASN D 29 ASN E 29 ASN F 250 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16374 Z= 0.418 Angle : 0.646 7.069 22338 Z= 0.347 Chirality : 0.050 0.175 2622 Planarity : 0.004 0.029 2856 Dihedral : 9.539 59.826 2324 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.64 % Allowed : 7.66 % Favored : 90.70 % 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: -0.21 (0.17), residues: 2058 helix: 0.10 (0.22), residues: 534 sheet: 0.05 (0.26), residues: 354 loop : -0.21 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 59 HIS 0.007 0.002 HIS D 250 PHE 0.016 0.002 PHE A 269 TYR 0.023 0.002 TYR D 231 ARG 0.007 0.001 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 53 time to evaluate : 1.743 Fit side-chains REVERT: B 210 MET cc_start: 0.7838 (ttm) cc_final: 0.7632 (ttm) REVERT: B 331 MET cc_start: 0.7376 (mmm) cc_final: 0.6999 (tpp) REVERT: C 219 MET cc_start: 0.8316 (ttp) cc_final: 0.7890 (ttm) REVERT: C 251 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5730 (mp) REVERT: F 186 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8558 (m) outliers start: 28 outliers final: 15 residues processed: 77 average time/residue: 0.2223 time to fit residues: 29.3176 Evaluate side-chains 61 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 124 optimal weight: 0.1980 chunk 186 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16374 Z= 0.137 Angle : 0.438 4.434 22338 Z= 0.239 Chirality : 0.044 0.157 2622 Planarity : 0.003 0.031 2856 Dihedral : 9.422 61.163 2322 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.11 % Allowed : 8.77 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2058 helix: 0.59 (0.23), residues: 528 sheet: 1.03 (0.29), residues: 318 loop : -0.20 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 333 HIS 0.005 0.001 HIS E 250 PHE 0.006 0.001 PHE E 342 TYR 0.013 0.001 TYR E 238 ARG 0.005 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 1.843 Fit side-chains REVERT: B 331 MET cc_start: 0.7408 (mmm) cc_final: 0.6797 (tpt) REVERT: C 331 MET cc_start: 0.7032 (tpp) cc_final: 0.6814 (tpt) REVERT: F 331 MET cc_start: 0.7252 (mmm) cc_final: 0.6330 (tpt) outliers start: 19 outliers final: 10 residues processed: 69 average time/residue: 0.2293 time to fit residues: 27.2038 Evaluate side-chains 55 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 2 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 168 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16374 Z= 0.199 Angle : 0.447 4.472 22338 Z= 0.242 Chirality : 0.044 0.153 2622 Planarity : 0.003 0.028 2856 Dihedral : 9.264 60.470 2322 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.29 % Allowed : 8.89 % Favored : 89.82 % 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: 0.36 (0.18), residues: 2058 helix: 0.71 (0.23), residues: 534 sheet: 1.12 (0.29), residues: 318 loop : -0.15 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 333 HIS 0.003 0.001 HIS E 96 PHE 0.008 0.001 PHE A 269 TYR 0.013 0.001 TYR B 238 ARG 0.005 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 1.781 Fit side-chains REVERT: B 331 MET cc_start: 0.7478 (mmm) cc_final: 0.6839 (tpt) REVERT: F 331 MET cc_start: 0.7294 (mmm) cc_final: 0.6269 (tpt) outliers start: 22 outliers final: 19 residues processed: 66 average time/residue: 0.2171 time to fit residues: 25.2995 Evaluate side-chains 63 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 44 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.6980 chunk 177 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16374 Z= 0.149 Angle : 0.419 4.966 22338 Z= 0.228 Chirality : 0.044 0.148 2622 Planarity : 0.003 0.028 2856 Dihedral : 9.238 60.776 2322 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.35 % Allowed : 9.18 % Favored : 89.47 % 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: 0.46 (0.18), residues: 2058 helix: 0.78 (0.23), residues: 534 sheet: 1.25 (0.30), residues: 318 loop : -0.12 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 333 HIS 0.002 0.001 HIS E 96 PHE 0.007 0.001 PHE A 269 TYR 0.012 0.001 TYR B 238 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 1.756 Fit side-chains REVERT: B 331 MET cc_start: 0.7493 (mmm) cc_final: 0.6852 (tpt) REVERT: F 201 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8392 (mt) REVERT: F 331 MET cc_start: 0.7272 (mmm) cc_final: 0.6480 (tpt) outliers start: 23 outliers final: 19 residues processed: 67 average time/residue: 0.2393 time to fit residues: 27.7922 Evaluate side-chains 64 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16374 Z= 0.182 Angle : 0.429 6.296 22338 Z= 0.232 Chirality : 0.044 0.147 2622 Planarity : 0.003 0.028 2856 Dihedral : 9.206 60.584 2322 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.58 % Allowed : 9.12 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2058 helix: 0.80 (0.23), residues: 534 sheet: 1.28 (0.30), residues: 318 loop : -0.10 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS E 96 PHE 0.008 0.001 PHE A 269 TYR 0.011 0.001 TYR B 238 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 44 time to evaluate : 1.921 Fit side-chains REVERT: B 331 MET cc_start: 0.7600 (mmm) cc_final: 0.7348 (tpt) REVERT: F 201 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8405 (mt) REVERT: F 331 MET cc_start: 0.7273 (mmm) cc_final: 0.6447 (tpt) outliers start: 27 outliers final: 21 residues processed: 70 average time/residue: 0.2019 time to fit residues: 25.5458 Evaluate side-chains 66 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 44 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.8980 chunk 78 optimal weight: 0.0000 chunk 117 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 178 optimal weight: 0.0670 overall best weight: 0.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 16374 Z= 0.106 Angle : 0.404 5.884 22338 Z= 0.220 Chirality : 0.043 0.145 2622 Planarity : 0.003 0.029 2856 Dihedral : 9.184 60.893 2322 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.29 % Allowed : 9.47 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 2058 helix: 0.85 (0.23), residues: 534 sheet: 1.60 (0.31), residues: 288 loop : -0.03 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.002 0.000 HIS E 96 PHE 0.006 0.001 PHE C 269 TYR 0.011 0.001 TYR A 226 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 51 time to evaluate : 1.991 Fit side-chains REVERT: B 331 MET cc_start: 0.7587 (mmm) cc_final: 0.7338 (tpt) REVERT: F 331 MET cc_start: 0.7195 (mmm) cc_final: 0.6424 (tpt) outliers start: 22 outliers final: 16 residues processed: 72 average time/residue: 0.2707 time to fit residues: 31.6956 Evaluate side-chains 61 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 233 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.0060 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 79 optimal weight: 0.0870 chunk 143 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 overall best weight: 1.1976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16374 Z= 0.153 Angle : 0.422 8.581 22338 Z= 0.228 Chirality : 0.044 0.145 2622 Planarity : 0.003 0.026 2856 Dihedral : 9.156 60.736 2322 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.23 % Allowed : 9.59 % Favored : 89.18 % 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: 0.63 (0.19), residues: 2058 helix: 0.85 (0.23), residues: 534 sheet: 1.45 (0.30), residues: 318 loop : 0.01 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS E 96 PHE 0.007 0.001 PHE A 269 TYR 0.012 0.001 TYR E 238 ARG 0.005 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 46 time to evaluate : 1.894 Fit side-chains REVERT: B 331 MET cc_start: 0.7597 (mmm) cc_final: 0.7343 (tpt) REVERT: E 219 MET cc_start: 0.7950 (mmt) cc_final: 0.7556 (mmp) REVERT: F 331 MET cc_start: 0.7198 (mmm) cc_final: 0.6427 (tpt) outliers start: 21 outliers final: 18 residues processed: 66 average time/residue: 0.2127 time to fit residues: 25.5487 Evaluate side-chains 64 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 46 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16374 Z= 0.147 Angle : 0.419 8.236 22338 Z= 0.226 Chirality : 0.044 0.145 2622 Planarity : 0.003 0.026 2856 Dihedral : 9.158 60.769 2322 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.23 % Allowed : 9.65 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 2058 helix: 0.84 (0.23), residues: 534 sheet: 1.48 (0.30), residues: 318 loop : 0.03 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 333 HIS 0.003 0.001 HIS E 96 PHE 0.007 0.001 PHE A 269 TYR 0.013 0.001 TYR E 238 ARG 0.005 0.000 ARG B 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 47 time to evaluate : 1.961 Fit side-chains REVERT: B 331 MET cc_start: 0.7617 (mmm) cc_final: 0.7369 (tpt) REVERT: F 331 MET cc_start: 0.7185 (mmm) cc_final: 0.6420 (tpt) outliers start: 21 outliers final: 18 residues processed: 67 average time/residue: 0.2286 time to fit residues: 27.2199 Evaluate side-chains 63 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 0.1980 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 142 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.063893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055322 restraints weight = 61026.494| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.64 r_work: 0.3242 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16374 Z= 0.150 Angle : 0.425 8.966 22338 Z= 0.228 Chirality : 0.044 0.145 2622 Planarity : 0.003 0.025 2856 Dihedral : 9.150 60.737 2322 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.23 % Allowed : 9.82 % Favored : 88.95 % 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: 0.66 (0.19), residues: 2058 helix: 0.83 (0.23), residues: 534 sheet: 1.52 (0.30), residues: 318 loop : 0.04 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 333 HIS 0.004 0.001 HIS D 243 PHE 0.007 0.001 PHE A 269 TYR 0.009 0.001 TYR D 226 ARG 0.005 0.000 ARG B 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.96 seconds wall clock time: 46 minutes 32.91 seconds (2792.91 seconds total)