Starting phenix.real_space_refine on Wed Mar 20 12:01:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bha_16050/03_2024/8bha_16050_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bha_16050/03_2024/8bha_16050.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bha_16050/03_2024/8bha_16050_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bha_16050/03_2024/8bha_16050_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bha_16050/03_2024/8bha_16050_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bha_16050/03_2024/8bha_16050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bha_16050/03_2024/8bha_16050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bha_16050/03_2024/8bha_16050_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bha_16050/03_2024/8bha_16050_trim_updated.pdb" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians S 90 5.16 5 C 8940 2.51 5 N 2275 2.21 5 O 2495 1.98 5 F 5 1.80 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27220 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'QI0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'QI0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'QI0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'QI0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'QI0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.67, per 1000 atoms: 0.43 Number of scatterers: 27220 At special positions: 0 Unit cell: (92.584, 91.28, 123.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 F 5 9.00 O 2495 8.00 N 2275 7.00 C 8940 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 21.82 Conformation dependent library (CDL) restraints added in 2.8 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 20 sheets defined 37.2% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 91 through 96 removed outlier: 4.262A pdb=" N SER A 95 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 234 through 249 removed outlier: 4.147A pdb=" N SER A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TRP A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 279 removed outlier: 4.233A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 312 Processing helix chain 'A' and resid 318 through 417 removed outlier: 4.017A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 16 through 26 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 91 through 96 removed outlier: 4.262A pdb=" N SER B 95 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 234 through 249 removed outlier: 4.147A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TRP B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 279 removed outlier: 4.233A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 318 through 417 removed outlier: 4.017A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 16 through 26 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 91 through 96 removed outlier: 4.262A pdb=" N SER C 95 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 181 No H-bonds generated for 'chain 'C' and resid 178 through 181' Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 234 through 249 removed outlier: 4.146A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TRP C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 279 removed outlier: 4.233A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 312 Processing helix chain 'C' and resid 318 through 417 removed outlier: 4.017A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 16 through 26 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 91 through 96 removed outlier: 4.262A pdb=" N SER D 95 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 181 No H-bonds generated for 'chain 'D' and resid 178 through 181' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 234 through 249 removed outlier: 4.147A pdb=" N SER D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TRP D 249 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 279 removed outlier: 4.233A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 312 Processing helix chain 'D' and resid 318 through 417 removed outlier: 4.017A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 16 through 26 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 91 through 96 removed outlier: 4.261A pdb=" N SER E 95 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 181 No H-bonds generated for 'chain 'E' and resid 178 through 181' Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 234 through 249 removed outlier: 4.147A pdb=" N SER E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE E 248 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TRP E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 279 removed outlier: 4.233A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 312 Processing helix chain 'E' and resid 318 through 417 removed outlier: 4.017A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.644A pdb=" N THR A 42 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL A 173 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL A 44 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 49 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 48 through 50 Processing sheet with id= C, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.760A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 107 through 112 removed outlier: 7.022A pdb=" N SER A 139 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER A 110 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A 137 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 170 through 174 removed outlier: 6.644A pdb=" N THR B 42 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL B 173 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL B 44 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 49 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 48 through 50 Processing sheet with id= G, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.761A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 107 through 112 removed outlier: 7.022A pdb=" N SER B 139 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER B 110 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR B 137 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 170 through 174 removed outlier: 6.644A pdb=" N THR C 42 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL C 173 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL C 44 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 49 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 48 through 50 Processing sheet with id= K, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.761A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 107 through 112 removed outlier: 7.021A pdb=" N SER C 139 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER C 110 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR C 137 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 170 through 174 removed outlier: 6.643A pdb=" N THR D 42 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL D 173 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL D 44 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 49 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 48 through 50 Processing sheet with id= O, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.761A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 107 through 112 removed outlier: 7.022A pdb=" N SER D 139 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N SER D 110 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR D 137 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 170 through 174 removed outlier: 6.644A pdb=" N THR E 42 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL E 173 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL E 44 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR E 49 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 48 through 50 Processing sheet with id= S, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.761A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 107 through 112 removed outlier: 7.022A pdb=" N SER E 139 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER E 110 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR E 137 " --> pdb=" O SER E 110 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1875 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: 9.89 Time building geometry restraints manager: 22.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 8 1.23 - 1.42: 6127 1.42 - 1.61: 7885 1.61 - 1.81: 160 Bond restraints: 27595 Sorted by residual: bond pdb=" C17 QI0 E 502 " pdb=" N2 QI0 E 502 " ideal model delta sigma weight residual 1.647 1.466 0.181 2.00e-02 2.50e+03 8.15e+01 bond pdb=" C17 QI0 A 502 " pdb=" N2 QI0 A 502 " ideal model delta sigma weight residual 1.647 1.467 0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" C17 QI0 D 502 " pdb=" N2 QI0 D 502 " ideal model delta sigma weight residual 1.647 1.467 0.180 2.00e-02 2.50e+03 8.09e+01 bond pdb=" C17 QI0 C 502 " pdb=" N2 QI0 C 502 " ideal model delta sigma weight residual 1.647 1.467 0.180 2.00e-02 2.50e+03 8.08e+01 bond pdb=" C17 QI0 B 502 " pdb=" N2 QI0 B 502 " ideal model delta sigma weight residual 1.647 1.468 0.179 2.00e-02 2.50e+03 8.03e+01 ... (remaining 27590 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.02: 463 107.02 - 113.77: 32031 113.77 - 120.51: 9274 120.51 - 127.25: 7622 127.25 - 134.00: 190 Bond angle restraints: 49580 Sorted by residual: angle pdb=" C1 QI0 B 502 " pdb=" C2 QI0 B 502 " pdb=" C10 QI0 B 502 " ideal model delta sigma weight residual 117.39 129.22 -11.83 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C1 QI0 D 502 " pdb=" C2 QI0 D 502 " pdb=" C10 QI0 D 502 " ideal model delta sigma weight residual 117.39 129.17 -11.78 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C1 QI0 E 502 " pdb=" C2 QI0 E 502 " pdb=" C10 QI0 E 502 " ideal model delta sigma weight residual 117.39 129.15 -11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C1 QI0 C 502 " pdb=" C2 QI0 C 502 " pdb=" C10 QI0 C 502 " ideal model delta sigma weight residual 117.39 129.14 -11.75 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C1 QI0 A 502 " pdb=" C2 QI0 A 502 " pdb=" C10 QI0 A 502 " ideal model delta sigma weight residual 117.39 129.14 -11.75 3.00e+00 1.11e-01 1.53e+01 ... (remaining 49575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 12645 17.25 - 34.49: 295 34.49 - 51.73: 139 51.73 - 68.98: 56 68.98 - 86.22: 5 Dihedral angle restraints: 13140 sinusoidal: 7010 harmonic: 6130 Sorted by residual: dihedral pdb=" CB MET B 115 " pdb=" CG MET B 115 " pdb=" SD MET B 115 " pdb=" CE MET B 115 " ideal model delta sinusoidal sigma weight residual 60.00 101.95 -41.95 3 1.50e+01 4.44e-03 7.52e+00 dihedral pdb=" CB MET E 115 " pdb=" CG MET E 115 " pdb=" SD MET E 115 " pdb=" CE MET E 115 " ideal model delta sinusoidal sigma weight residual 60.00 101.95 -41.95 3 1.50e+01 4.44e-03 7.52e+00 dihedral pdb=" CB MET D 115 " pdb=" CG MET D 115 " pdb=" SD MET D 115 " pdb=" CE MET D 115 " ideal model delta sinusoidal sigma weight residual 60.00 101.94 -41.94 3 1.50e+01 4.44e-03 7.52e+00 ... (remaining 13137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 1184 0.023 - 0.047: 623 0.047 - 0.070: 180 0.070 - 0.093: 86 0.093 - 0.116: 87 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE D 41 " pdb=" N ILE D 41 " pdb=" C ILE D 41 " pdb=" CB ILE D 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE E 41 " pdb=" N ILE E 41 " pdb=" C ILE E 41 " pdb=" CB ILE E 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA ILE A 41 " pdb=" N ILE A 41 " pdb=" C ILE A 41 " pdb=" CB ILE A 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.31e-01 ... (remaining 2157 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 QI0 A 502 " -0.011 2.00e-02 2.50e+03 2.72e-02 1.48e+01 pdb=" C12 QI0 A 502 " -0.018 2.00e-02 2.50e+03 pdb=" C13 QI0 A 502 " -0.010 2.00e-02 2.50e+03 pdb=" C14 QI0 A 502 " -0.017 2.00e-02 2.50e+03 pdb=" C15 QI0 A 502 " -0.018 2.00e-02 2.50e+03 pdb=" C16 QI0 A 502 " 0.045 2.00e-02 2.50e+03 pdb=" N1 QI0 A 502 " -0.018 2.00e-02 2.50e+03 pdb=" O1 QI0 A 502 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QI0 E 502 " 0.011 2.00e-02 2.50e+03 2.71e-02 1.47e+01 pdb=" C12 QI0 E 502 " 0.018 2.00e-02 2.50e+03 pdb=" C13 QI0 E 502 " 0.011 2.00e-02 2.50e+03 pdb=" C14 QI0 E 502 " 0.016 2.00e-02 2.50e+03 pdb=" C15 QI0 E 502 " 0.019 2.00e-02 2.50e+03 pdb=" C16 QI0 E 502 " -0.045 2.00e-02 2.50e+03 pdb=" N1 QI0 E 502 " 0.018 2.00e-02 2.50e+03 pdb=" O1 QI0 E 502 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QI0 B 502 " -0.011 2.00e-02 2.50e+03 2.71e-02 1.47e+01 pdb=" C12 QI0 B 502 " -0.018 2.00e-02 2.50e+03 pdb=" C13 QI0 B 502 " -0.010 2.00e-02 2.50e+03 pdb=" C14 QI0 B 502 " -0.017 2.00e-02 2.50e+03 pdb=" C15 QI0 B 502 " -0.019 2.00e-02 2.50e+03 pdb=" C16 QI0 B 502 " 0.044 2.00e-02 2.50e+03 pdb=" N1 QI0 B 502 " -0.018 2.00e-02 2.50e+03 pdb=" O1 QI0 B 502 " 0.049 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 5163 2.30 - 2.88: 62670 2.88 - 3.45: 69179 3.45 - 4.03: 100221 4.03 - 4.60: 151251 Nonbonded interactions: 388484 Sorted by model distance: nonbonded pdb=" OD2 ASP B 101 " pdb=" H ALA B 164 " model vdw 1.725 1.850 nonbonded pdb=" OD2 ASP C 101 " pdb=" H ALA C 164 " model vdw 1.725 1.850 nonbonded pdb=" OD2 ASP E 101 " pdb=" H ALA E 164 " model vdw 1.725 1.850 nonbonded pdb=" OD2 ASP D 101 " pdb=" H ALA D 164 " model vdw 1.726 1.850 nonbonded pdb=" OD2 ASP A 101 " pdb=" H ALA A 164 " model vdw 1.726 1.850 ... (remaining 388479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 8.670 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: 0.410 Extract box with map and model: 29.980 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 83.450 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.181 14180 Z= 0.498 Angle : 0.581 11.829 19305 Z= 0.239 Chirality : 0.037 0.116 2160 Planarity : 0.003 0.028 2395 Dihedral : 7.905 86.225 5130 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 2.00 (0.22), residues: 1670 helix: 2.74 (0.21), residues: 585 sheet: 0.44 (0.27), residues: 435 loop : 0.77 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 414 HIS 0.003 0.001 HIS B 195 PHE 0.007 0.001 PHE E 104 TYR 0.006 0.001 TYR B 285 ARG 0.002 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 2.9350 time to fit residues: 747.4864 Evaluate side-chains 132 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN B 232 GLN C 232 GLN D 232 GLN E 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14180 Z= 0.180 Angle : 0.471 5.956 19305 Z= 0.242 Chirality : 0.040 0.160 2160 Planarity : 0.004 0.059 2395 Dihedral : 4.018 34.476 1995 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.41 % Allowed : 6.51 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 2.13 (0.22), residues: 1670 helix: 3.15 (0.22), residues: 575 sheet: 0.56 (0.27), residues: 435 loop : 0.53 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 73 HIS 0.003 0.001 HIS D 221 PHE 0.010 0.001 PHE D 111 TYR 0.008 0.001 TYR B 413 ARG 0.008 0.000 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.706 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: C 151 MET cc_start: 0.8647 (mpt) cc_final: 0.8335 (mpt) REVERT: D 60 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8302 (mt-10) outliers start: 21 outliers final: 5 residues processed: 151 average time/residue: 2.4478 time to fit residues: 409.6869 Evaluate side-chains 131 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 14180 Z= 0.286 Angle : 0.484 6.283 19305 Z= 0.250 Chirality : 0.041 0.163 2160 Planarity : 0.004 0.036 2395 Dihedral : 4.114 30.485 1995 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.08 % Allowed : 6.31 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.79 (0.21), residues: 1670 helix: 2.87 (0.22), residues: 580 sheet: 0.20 (0.25), residues: 465 loop : 0.46 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 73 HIS 0.004 0.001 HIS B 221 PHE 0.011 0.002 PHE C 69 TYR 0.009 0.001 TYR A 413 ARG 0.005 0.000 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 2.293 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 395 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8495 (m-30) REVERT: C 151 MET cc_start: 0.8916 (mpt) cc_final: 0.8687 (mpt) REVERT: D 60 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8290 (mt-10) outliers start: 31 outliers final: 11 residues processed: 139 average time/residue: 2.5447 time to fit residues: 391.0934 Evaluate side-chains 129 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.0040 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- 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: 0.8782 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14180 Z= 0.244 Angle : 0.463 6.047 19305 Z= 0.238 Chirality : 0.040 0.161 2160 Planarity : 0.004 0.034 2395 Dihedral : 4.030 29.088 1995 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.88 % Allowed : 6.85 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.69 (0.21), residues: 1670 helix: 2.88 (0.22), residues: 580 sheet: 0.05 (0.24), residues: 465 loop : 0.40 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 73 HIS 0.003 0.001 HIS E 221 PHE 0.008 0.001 PHE A 307 TYR 0.007 0.001 TYR E 413 ARG 0.003 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 2.095 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 395 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8464 (m-30) REVERT: B 47 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8148 (p0) REVERT: B 277 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.8011 (mmt90) REVERT: C 47 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8050 (p0) REVERT: D 60 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8291 (mt-10) outliers start: 28 outliers final: 5 residues processed: 135 average time/residue: 2.6286 time to fit residues: 391.1947 Evaluate side-chains 126 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.8783 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 14180 Z= 0.240 Angle : 0.463 6.188 19305 Z= 0.237 Chirality : 0.040 0.164 2160 Planarity : 0.004 0.039 2395 Dihedral : 4.019 29.272 1995 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.81 % Allowed : 6.91 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.67 (0.21), residues: 1670 helix: 2.89 (0.22), residues: 580 sheet: 0.09 (0.24), residues: 460 loop : 0.30 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 114 HIS 0.003 0.001 HIS B 221 PHE 0.008 0.001 PHE D 104 TYR 0.007 0.001 TYR A 413 ARG 0.003 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 2.233 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 395 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8467 (m-30) REVERT: B 277 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.8003 (mmt90) REVERT: D 60 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8291 (mt-10) outliers start: 27 outliers final: 8 residues processed: 132 average time/residue: 2.7011 time to fit residues: 393.0970 Evaluate side-chains 126 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 277 ARG Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 14180 Z= 0.327 Angle : 0.500 6.930 19305 Z= 0.256 Chirality : 0.041 0.164 2160 Planarity : 0.004 0.040 2395 Dihedral : 4.263 26.756 1995 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.68 % Allowed : 7.05 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.51 (0.21), residues: 1670 helix: 2.78 (0.22), residues: 580 sheet: -0.05 (0.24), residues: 460 loop : 0.23 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 114 HIS 0.003 0.001 HIS E 221 PHE 0.010 0.001 PHE E 104 TYR 0.008 0.001 TYR A 413 ARG 0.004 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: B 245 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8906 (mt0) REVERT: B 251 ASN cc_start: 0.8262 (m-40) cc_final: 0.7970 (t0) REVERT: D 60 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8285 (mt-10) outliers start: 25 outliers final: 9 residues processed: 135 average time/residue: 2.6156 time to fit residues: 390.3016 Evaluate side-chains 124 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8792 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14180 Z= 0.251 Angle : 0.477 7.212 19305 Z= 0.243 Chirality : 0.040 0.183 2160 Planarity : 0.004 0.043 2395 Dihedral : 4.098 28.202 1995 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.28 % Allowed : 7.38 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.51 (0.21), residues: 1670 helix: 2.80 (0.22), residues: 580 sheet: -0.10 (0.24), residues: 460 loop : 0.25 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.002 0.001 HIS E 221 PHE 0.008 0.001 PHE B 104 TYR 0.007 0.001 TYR A 413 ARG 0.004 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 2.132 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 395 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: B 245 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8756 (mt0) REVERT: B 251 ASN cc_start: 0.8236 (m-40) cc_final: 0.7970 (t0) REVERT: D 60 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8269 (mt-10) outliers start: 19 outliers final: 12 residues processed: 125 average time/residue: 2.6688 time to fit residues: 367.6642 Evaluate side-chains 128 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.0050 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14180 Z= 0.215 Angle : 0.462 6.884 19305 Z= 0.235 Chirality : 0.040 0.193 2160 Planarity : 0.004 0.044 2395 Dihedral : 3.997 29.581 1995 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.07 % Allowed : 7.58 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.56 (0.21), residues: 1670 helix: 2.86 (0.22), residues: 580 sheet: -0.08 (0.24), residues: 455 loop : 0.27 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.002 0.001 HIS E 221 PHE 0.008 0.001 PHE B 261 TYR 0.007 0.001 TYR A 413 ARG 0.004 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 2.146 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 395 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8377 (m-30) REVERT: D 60 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8277 (mt-10) REVERT: E 43 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8528 (tt0) outliers start: 16 outliers final: 10 residues processed: 122 average time/residue: 2.6660 time to fit residues: 359.4768 Evaluate side-chains 124 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 315 LYS Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 0.1980 chunk 147 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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: 0.8760 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14180 Z= 0.147 Angle : 0.437 7.081 19305 Z= 0.220 Chirality : 0.039 0.161 2160 Planarity : 0.004 0.042 2395 Dihedral : 3.783 32.914 1995 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.60 % Allowed : 8.26 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.73 (0.21), residues: 1670 helix: 3.02 (0.21), residues: 580 sheet: -0.04 (0.24), residues: 460 loop : 0.38 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 114 HIS 0.002 0.001 HIS A 105 PHE 0.007 0.001 PHE C 261 TYR 0.007 0.001 TYR E 413 ARG 0.005 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: B 60 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8137 (mt-10) REVERT: D 60 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8291 (mt-10) REVERT: E 43 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: E 60 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8121 (mt-10) outliers start: 9 outliers final: 4 residues processed: 118 average time/residue: 2.6795 time to fit residues: 348.2954 Evaluate side-chains 116 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.8774 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14180 Z= 0.204 Angle : 0.464 8.135 19305 Z= 0.232 Chirality : 0.040 0.214 2160 Planarity : 0.004 0.040 2395 Dihedral : 3.919 31.055 1995 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.67 % Allowed : 8.26 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.71 (0.21), residues: 1670 helix: 3.03 (0.22), residues: 580 sheet: -0.07 (0.24), residues: 460 loop : 0.37 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 114 HIS 0.005 0.001 HIS A 105 PHE 0.008 0.001 PHE A 18 TYR 0.007 0.001 TYR A 413 ARG 0.005 0.000 ARG E 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 2.352 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 395 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: D 60 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8286 (mt-10) REVERT: E 43 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: E 60 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8111 (mt-10) outliers start: 10 outliers final: 6 residues processed: 117 average time/residue: 2.7208 time to fit residues: 350.6301 Evaluate side-chains 119 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.0040 chunk 54 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.073849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.062741 restraints weight = 79748.600| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.41 r_work: 0.2768 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14180 Z= 0.196 Angle : 0.459 8.383 19305 Z= 0.230 Chirality : 0.039 0.195 2160 Planarity : 0.004 0.036 2395 Dihedral : 3.880 30.839 1995 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.67 % Allowed : 8.19 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.71 (0.21), residues: 1670 helix: 3.04 (0.21), residues: 580 sheet: -0.07 (0.24), residues: 460 loop : 0.36 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 114 HIS 0.005 0.001 HIS A 105 PHE 0.009 0.001 PHE E 18 TYR 0.007 0.001 TYR A 413 ARG 0.004 0.000 ARG C 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8269.93 seconds wall clock time: 145 minutes 48.24 seconds (8748.24 seconds total)