Starting phenix.real_space_refine on Mon May 4 00:46:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9trm_56179/05_2026/9trm_56179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9trm_56179/05_2026/9trm_56179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9trm_56179/05_2026/9trm_56179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9trm_56179/05_2026/9trm_56179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9trm_56179/05_2026/9trm_56179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9trm_56179/05_2026/9trm_56179.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 sd= 0.093 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 Ca 12 9.91 5 P 53 5.49 5 S 88 5.16 5 C 10242 2.51 5 N 2940 2.21 5 O 3261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16596 Number of models: 1 Model: "" Number of chains: 21 Chain: "O" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 524 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain breaks: 1 Chain: "X" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "Z" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 139 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 149 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Chain: "E" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 143 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 149 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Chain: "F" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 139 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 149 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Chain: "I" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "J" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "K" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "L" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "M" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2380 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2374 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.18, per 1000 atoms: 0.25 Number of scatterers: 16596 At special positions: 0 Unit cell: (126.84, 112.56, 161.28, 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) Ca 12 19.99 S 88 16.00 P 53 15.00 O 3261 8.00 N 2940 7.00 C 10242 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: 1.21 Conformation dependent library (CDL) restraints added in 704.4 milliseconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 19 sheets defined 51.5% alpha, 16.9% beta 16 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Proline residue: A 7 - end of helix Processing helix chain 'B' and resid 2 through 10 removed outlier: 3.745A pdb=" N ALA B 6 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Proline residue: B 7 - end of helix removed outlier: 3.537A pdb=" N LEU B 10 " --> pdb=" O PRO B 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Proline residue: E 7 - end of helix Processing helix chain 'C' and resid 2 through 10 Proline residue: C 7 - end of helix Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'I' and resid 24 through 31 Processing helix chain 'I' and resid 34 through 43 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 56 through 62 Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.567A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 98 removed outlier: 3.754A pdb=" N GLU I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 132 through 144 removed outlier: 3.595A pdb=" N VAL I 142 " --> pdb=" O HIS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.872A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 196 through 214 removed outlier: 3.907A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN I 206 " --> pdb=" O GLN I 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 232 removed outlier: 4.027A pdb=" N THR I 230 " --> pdb=" O ALA I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 237 through 260 Processing helix chain 'I' and resid 288 through 296 removed outlier: 3.723A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 32 removed outlier: 3.817A pdb=" N GLN J 30 " --> pdb=" O SER J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 45 Processing helix chain 'J' and resid 48 through 55 Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'J' and resid 67 through 80 Processing helix chain 'J' and resid 89 through 98 removed outlier: 4.179A pdb=" N GLU J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 113 Processing helix chain 'J' and resid 132 through 144 removed outlier: 3.620A pdb=" N VAL J 142 " --> pdb=" O HIS J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 178 removed outlier: 3.828A pdb=" N LEU J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 188 Processing helix chain 'J' and resid 196 through 212 removed outlier: 3.987A pdb=" N LEU J 204 " --> pdb=" O GLN J 200 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR J 205 " --> pdb=" O THR J 201 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN J 206 " --> pdb=" O GLN J 202 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA J 209 " --> pdb=" O TYR J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 232 removed outlier: 3.998A pdb=" N THR J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 237 through 260 Processing helix chain 'J' and resid 288 through 296 removed outlier: 3.673A pdb=" N ILE J 292 " --> pdb=" O GLY J 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 32 removed outlier: 3.678A pdb=" N GLY K 32 " --> pdb=" O GLU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 55 Processing helix chain 'K' and resid 56 through 62 removed outlier: 3.545A pdb=" N ASN K 62 " --> pdb=" O LYS K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.559A pdb=" N LEU K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 97 Processing helix chain 'K' and resid 106 through 114 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.598A pdb=" N VAL K 142 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 178 removed outlier: 3.733A pdb=" N LEU K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 214 removed outlier: 3.778A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 232 removed outlier: 3.951A pdb=" N THR K 230 " --> pdb=" O ALA K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 236 No H-bonds generated for 'chain 'K' and resid 234 through 236' Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 288 through 296 removed outlier: 3.727A pdb=" N ILE K 292 " --> pdb=" O GLY K 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 30 Processing helix chain 'L' and resid 34 through 44 Processing helix chain 'L' and resid 48 through 55 Processing helix chain 'L' and resid 56 through 63 removed outlier: 3.775A pdb=" N ILE L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 Processing helix chain 'L' and resid 89 through 97 Processing helix chain 'L' and resid 106 through 114 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.523A pdb=" N VAL L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 146 No H-bonds generated for 'chain 'L' and resid 145 through 146' Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 179 removed outlier: 3.829A pdb=" N LEU L 171 " --> pdb=" O ARG L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 214 removed outlier: 4.010A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA L 209 " --> pdb=" O TYR L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 232 removed outlier: 3.923A pdb=" N THR L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 236 No H-bonds generated for 'chain 'L' and resid 234 through 236' Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 288 through 296 removed outlier: 3.618A pdb=" N ILE L 292 " --> pdb=" O GLY L 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 31 removed outlier: 3.547A pdb=" N GLN M 30 " --> pdb=" O SER M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 44 removed outlier: 3.628A pdb=" N ALA M 44 " --> pdb=" O LYS M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 54 Processing helix chain 'M' and resid 56 through 63 removed outlier: 3.810A pdb=" N LEU M 60 " --> pdb=" O PRO M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 82 Processing helix chain 'M' and resid 89 through 97 Processing helix chain 'M' and resid 107 through 113 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.520A pdb=" N VAL M 142 " --> pdb=" O HIS M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 179 removed outlier: 3.865A pdb=" N LEU M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 214 removed outlier: 3.974A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 232 removed outlier: 3.514A pdb=" N TYR M 232 " --> pdb=" O TYR M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 288 through 296 removed outlier: 3.832A pdb=" N ILE M 292 " --> pdb=" O GLY M 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 32 removed outlier: 4.043A pdb=" N GLU N 29 " --> pdb=" O ILE N 25 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN N 30 " --> pdb=" O SER N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 45 Processing helix chain 'N' and resid 48 through 54 Processing helix chain 'N' and resid 56 through 63 removed outlier: 3.596A pdb=" N LEU N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE N 63 " --> pdb=" O GLU N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 82 removed outlier: 3.673A pdb=" N LEU N 81 " --> pdb=" O GLU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 97 removed outlier: 3.716A pdb=" N PHE N 92 " --> pdb=" O THR N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 114 Processing helix chain 'N' and resid 132 through 144 Processing helix chain 'N' and resid 145 through 146 No H-bonds generated for 'chain 'N' and resid 145 through 146' Processing helix chain 'N' and resid 147 through 151 Processing helix chain 'N' and resid 167 through 178 removed outlier: 3.648A pdb=" N LEU N 171 " --> pdb=" O ARG N 167 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR N 178 " --> pdb=" O VAL N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 214 removed outlier: 3.644A pdb=" N THR N 201 " --> pdb=" O THR N 197 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA N 209 " --> pdb=" O TYR N 205 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL N 212 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER N 214 " --> pdb=" O MET N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 232 Processing helix chain 'N' and resid 234 through 236 No H-bonds generated for 'chain 'N' and resid 234 through 236' Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 288 through 294 removed outlier: 3.651A pdb=" N ILE N 292 " --> pdb=" O GLY N 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 42 through 44 removed outlier: 3.735A pdb=" N GLY O 44 " --> pdb=" O LEU O 35 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY O 22 " --> pdb=" O TRP O 9 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR O 4 " --> pdb=" O VAL O 75 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL O 75 " --> pdb=" O TYR O 4 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER O 6 " --> pdb=" O MET O 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 87 through 88 removed outlier: 6.615A pdb=" N ALA J 157 " --> pdb=" O ALA J 190 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ALA J 192 " --> pdb=" O ALA J 157 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR J 159 " --> pdb=" O ALA J 192 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS J 156 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU J 218 " --> pdb=" O LYS J 156 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA J 217 " --> pdb=" O ALA J 262 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL J 264 " --> pdb=" O ALA J 217 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU J 219 " --> pdb=" O VAL J 264 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR J 266 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL J 221 " --> pdb=" O THR J 266 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY J 127 " --> pdb=" O ASN J 267 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE J 122 " --> pdb=" O THR J 298 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU J 300 " --> pdb=" O ILE J 122 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU J 124 " --> pdb=" O LEU J 300 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU J 302 " --> pdb=" O GLU J 124 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE J 126 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N LYS J 304 " --> pdb=" O PHE J 126 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG J 299 " --> pdb=" O TYR J 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'I' and resid 189 through 193 removed outlier: 6.679A pdb=" N LYS I 156 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ILE I 220 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET I 158 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASP I 222 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE I 160 " --> pdb=" O ASP I 222 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY I 333 " --> pdb=" O ASN I 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AA6, first strand: chain 'J' and resid 87 through 88 removed outlier: 5.546A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU K 218 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AA8, first strand: chain 'J' and resid 269 through 271 Processing sheet with id=AA9, first strand: chain 'K' and resid 87 through 88 removed outlier: 6.921A pdb=" N LYS L 156 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU L 219 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET L 158 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL L 221 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE L 160 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE L 122 " --> pdb=" O THR L 298 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU L 300 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU L 124 " --> pdb=" O LEU L 300 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU L 302 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE L 126 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N LYS L 304 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 101 through 102 Processing sheet with id=AB2, first strand: chain 'K' and resid 269 through 271 Processing sheet with id=AB3, first strand: chain 'L' and resid 87 through 88 removed outlier: 6.627A pdb=" N LYS M 156 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ILE M 220 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET M 158 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP M 222 " --> pdb=" O MET M 158 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE M 160 " --> pdb=" O ASP M 222 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 101 through 102 Processing sheet with id=AB5, first strand: chain 'L' and resid 269 through 271 Processing sheet with id=AB6, first strand: chain 'M' and resid 87 through 88 removed outlier: 6.688A pdb=" N ALA N 157 " --> pdb=" O ALA N 190 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ALA N 192 " --> pdb=" O ALA N 157 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR N 159 " --> pdb=" O ALA N 192 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS N 156 " --> pdb=" O TYR N 216 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU N 218 " --> pdb=" O LYS N 156 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY N 127 " --> pdb=" O ASN N 267 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 101 through 102 Processing sheet with id=AB8, first strand: chain 'M' and resid 269 through 271 Processing sheet with id=AB9, first strand: chain 'N' and resid 101 through 102 Processing sheet with id=AC1, first strand: chain 'N' and resid 269 through 271 788 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4299 1.33 - 1.45: 2962 1.45 - 1.57: 9407 1.57 - 1.69: 98 1.69 - 1.81: 144 Bond restraints: 16910 Sorted by residual: bond pdb=" C ARG E 2 " pdb=" N ARG E 3 " ideal model delta sigma weight residual 1.334 1.259 0.075 1.46e-02 4.69e+03 2.67e+01 bond pdb=" C ACE E 0 " pdb=" N MET E 1 " ideal model delta sigma weight residual 1.329 1.420 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C ACE B 0 " pdb=" N MET B 1 " ideal model delta sigma weight residual 1.329 1.418 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C ACE F 0 " pdb=" N MET F 1 " ideal model delta sigma weight residual 1.329 1.418 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C ACE C 0 " pdb=" N MET C 1 " ideal model delta sigma weight residual 1.329 1.417 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 16905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 22795 2.85 - 5.70: 150 5.70 - 8.55: 15 8.55 - 11.41: 6 11.41 - 14.26: 1 Bond angle restraints: 22967 Sorted by residual: angle pdb=" N ARG E 3 " pdb=" CA ARG E 3 " pdb=" C ARG E 3 " ideal model delta sigma weight residual 112.23 97.97 14.26 1.26e+00 6.30e-01 1.28e+02 angle pdb=" C ASP I 37 " pdb=" CA ASP I 37 " pdb=" CB ASP I 37 " ideal model delta sigma weight residual 110.85 121.52 -10.67 1.70e+00 3.46e-01 3.94e+01 angle pdb=" O ARG E 2 " pdb=" C ARG E 2 " pdb=" N ARG E 3 " ideal model delta sigma weight residual 122.59 115.30 7.29 1.33e+00 5.65e-01 3.00e+01 angle pdb=" C ARG E 2 " pdb=" N ARG E 3 " pdb=" CA ARG E 3 " ideal model delta sigma weight residual 120.68 129.95 -9.27 1.70e+00 3.46e-01 2.97e+01 angle pdb=" N ARG E 3 " pdb=" CA ARG E 3 " pdb=" CB ARG E 3 " ideal model delta sigma weight residual 110.30 118.68 -8.38 1.54e+00 4.22e-01 2.96e+01 ... (remaining 22962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8776 17.95 - 35.90: 1054 35.90 - 53.86: 373 53.86 - 71.81: 112 71.81 - 89.76: 21 Dihedral angle restraints: 10336 sinusoidal: 4514 harmonic: 5822 Sorted by residual: dihedral pdb=" CA ARG E 2 " pdb=" C ARG E 2 " pdb=" N ARG E 3 " pdb=" CA ARG E 3 " ideal model delta harmonic sigma weight residual -180.00 -152.10 -27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" C ASP I 37 " pdb=" N ASP I 37 " pdb=" CA ASP I 37 " pdb=" CB ASP I 37 " ideal model delta harmonic sigma weight residual -122.60 -133.35 10.75 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" CA PRO N 24 " pdb=" C PRO N 24 " pdb=" N ILE N 25 " pdb=" CA ILE N 25 " ideal model delta harmonic sigma weight residual -180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 10333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2178 0.052 - 0.105: 366 0.105 - 0.157: 51 0.157 - 0.209: 3 0.209 - 0.262: 1 Chirality restraints: 2599 Sorted by residual: chirality pdb=" CA ASP I 37 " pdb=" N ASP I 37 " pdb=" C ASP I 37 " pdb=" CB ASP I 37 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL I 38 " pdb=" CA VAL I 38 " pdb=" CG1 VAL I 38 " pdb=" CG2 VAL I 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA ALA I 35 " pdb=" N ALA I 35 " pdb=" C ALA I 35 " pdb=" CB ALA I 35 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 2596 not shown) Planarity restraints: 2825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 2 " 0.026 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C ARG E 2 " -0.087 2.00e-02 2.50e+03 pdb=" O ARG E 2 " 0.031 2.00e-02 2.50e+03 pdb=" N ARG E 3 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 38 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C VAL I 38 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL I 38 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS I 39 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN N 23 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO N 24 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO N 24 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO N 24 " -0.026 5.00e-02 4.00e+02 ... (remaining 2822 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4373 2.81 - 3.33: 14265 3.33 - 3.86: 26991 3.86 - 4.38: 34069 4.38 - 4.90: 55590 Nonbonded interactions: 135288 Sorted by model distance: nonbonded pdb=" O2G ATP J 401 " pdb="CA CA J 402 " model vdw 2.290 2.510 nonbonded pdb=" O2B ATP K 401 " pdb="CA CA K 402 " model vdw 2.293 2.510 nonbonded pdb=" O2B ATP L 401 " pdb="CA CA L 402 " model vdw 2.336 2.510 nonbonded pdb=" O SER L 26 " pdb=" OE1 GLU L 29 " model vdw 2.352 3.040 nonbonded pdb=" O3G ATP M 401 " pdb="CA CA M 402 " model vdw 2.367 2.510 ... (remaining 135283 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' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26)) selection = (chain 'C' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26)) selection = (chain 'D' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26)) selection = (chain 'E' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 26)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 21 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 112 or (resid 113 through 114 and \ (name N or name CA or name C or name O or name CB )) or resid 115 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 3 through 402)) selection = (chain 'J' and (resid 21 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 112 or (resid 113 through 114 and \ (name N or name CA or name C or name O or name CB )) or resid 115 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 3 through 402)) selection = (chain 'K' and (resid 21 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 112 or (resid 113 through 114 and \ (name N or name CA or name C or name O or name CB )) or resid 115 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 3 through 402)) selection = (chain 'L' and (resid 21 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 112 or (resid 113 through 114 and \ (name N or name CA or name C or name O or name CB )) or resid 115 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 3 through 402)) selection = (chain 'M' and (resid 21 through 112 or (resid 113 through 114 and (name N or na \ me CA or name C or name O or name CB )) or resid 115 through 331 or (resid 332 a \ nd (name N or name CA or name C or name O or name CB )) or resid 333 through 402 \ )) selection = (chain 'N' and (resid 21 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 402)) } 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: 3.230 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.660 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 16910 Z= 0.178 Angle : 0.608 14.256 22967 Z= 0.330 Chirality : 0.040 0.262 2599 Planarity : 0.005 0.050 2825 Dihedral : 18.381 89.760 6596 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.50 % Favored : 98.45 % Rotamer: Outliers : 1.04 % Allowed : 25.58 % Favored : 73.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 1995 helix: 1.15 (0.18), residues: 834 sheet: 0.81 (0.28), residues: 358 loop : -0.51 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 27 TYR 0.018 0.001 TYR L 315 PHE 0.030 0.002 PHE E 20 TRP 0.006 0.001 TRP O 20 HIS 0.002 0.001 HIS O 17 Details of bonding type rmsd covalent geometry : bond 0.00353 (16910) covalent geometry : angle 0.60830 (22967) hydrogen bonds : bond 0.15923 ( 827) hydrogen bonds : angle 6.28502 ( 2262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 282 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: I 178 TYR cc_start: 0.8624 (m-80) cc_final: 0.8412 (m-80) REVERT: I 184 ASP cc_start: 0.6877 (m-30) cc_final: 0.6649 (m-30) REVERT: L 62 ASN cc_start: 0.8126 (m-40) cc_final: 0.7911 (m110) REVERT: N 27 ARG cc_start: 0.6971 (mpt180) cc_final: 0.6693 (mpt180) REVERT: N 82 VAL cc_start: 0.7647 (t) cc_final: 0.7394 (t) REVERT: N 84 MET cc_start: 0.6094 (mmm) cc_final: 0.5446 (tpt) outliers start: 17 outliers final: 6 residues processed: 292 average time/residue: 0.8440 time to fit residues: 265.9395 Evaluate side-chains 214 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 208 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 45 ARG Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 38 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN J 30 GLN K 30 GLN M 199 HIS N 101 GLN N 200 GLN N 272 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.118423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.090152 restraints weight = 24552.720| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.92 r_work: 0.3148 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16910 Z= 0.151 Angle : 0.532 7.790 22967 Z= 0.288 Chirality : 0.041 0.145 2599 Planarity : 0.004 0.041 2825 Dihedral : 13.005 85.254 2834 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.87 % Allowed : 22.89 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 1995 helix: 1.30 (0.18), residues: 840 sheet: 0.52 (0.27), residues: 385 loop : -0.36 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 27 TYR 0.017 0.001 TYR J 315 PHE 0.016 0.002 PHE F 20 TRP 0.003 0.001 TRP O 20 HIS 0.003 0.001 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00336 (16910) covalent geometry : angle 0.53214 (22967) hydrogen bonds : bond 0.04338 ( 827) hydrogen bonds : angle 4.85201 ( 2262) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 0.635 Fit side-chains REVERT: O 5 PHE cc_start: 0.7979 (m-80) cc_final: 0.7738 (m-80) REVERT: O 11 LYS cc_start: 0.8625 (tptp) cc_final: 0.8238 (tptp) REVERT: O 36 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6637 (tptp) REVERT: O 69 GLU cc_start: 0.8326 (tp30) cc_final: 0.7922 (mp0) REVERT: O 71 GLU cc_start: 0.8249 (tt0) cc_final: 0.7922 (tm-30) REVERT: I 111 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8709 (ttmm) REVERT: I 184 ASP cc_start: 0.8110 (m-30) cc_final: 0.7732 (m-30) REVERT: K 306 ARG cc_start: 0.8185 (mmt90) cc_final: 0.7922 (mmp-170) REVERT: M 72 ASP cc_start: 0.8566 (m-30) cc_final: 0.8241 (m-30) REVERT: N 27 ARG cc_start: 0.7026 (mpt180) cc_final: 0.6678 (mpt180) REVERT: N 84 MET cc_start: 0.5771 (mmm) cc_final: 0.5099 (tpt) REVERT: N 176 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7747 (tp30) outliers start: 47 outliers final: 13 residues processed: 250 average time/residue: 0.8397 time to fit residues: 227.4640 Evaluate side-chains 216 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain I residue 111 LYS Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Chi-restraints excluded: chain N residue 211 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 199 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN J 30 GLN L 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.115885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.088292 restraints weight = 24907.782| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.88 r_work: 0.3108 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16910 Z= 0.210 Angle : 0.564 8.788 22967 Z= 0.305 Chirality : 0.043 0.137 2599 Planarity : 0.004 0.042 2825 Dihedral : 13.216 88.554 2827 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.42 % Allowed : 21.61 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1995 helix: 1.25 (0.18), residues: 840 sheet: 0.47 (0.26), residues: 385 loop : -0.38 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 27 TYR 0.019 0.002 TYR L 315 PHE 0.016 0.002 PHE F 20 TRP 0.005 0.001 TRP O 9 HIS 0.005 0.001 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00492 (16910) covalent geometry : angle 0.56427 (22967) hydrogen bonds : bond 0.05068 ( 827) hydrogen bonds : angle 4.81303 ( 2262) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 0.673 Fit side-chains REVERT: O 5 PHE cc_start: 0.7964 (m-80) cc_final: 0.7553 (m-80) REVERT: O 36 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6587 (tptp) REVERT: O 71 GLU cc_start: 0.8221 (tt0) cc_final: 0.8007 (tm-30) REVERT: I 26 SER cc_start: 0.7943 (OUTLIER) cc_final: 0.7403 (p) REVERT: I 39 LYS cc_start: 0.8453 (mtpm) cc_final: 0.8005 (mmmt) REVERT: I 111 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8767 (ttmm) REVERT: I 184 ASP cc_start: 0.8158 (m-30) cc_final: 0.7779 (m-30) REVERT: I 326 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8811 (ttm) REVERT: K 306 ARG cc_start: 0.8165 (mmt90) cc_final: 0.7892 (mmp-170) REVERT: L 61 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8127 (mp) REVERT: L 213 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: M 27 ARG cc_start: 0.7579 (mpt90) cc_final: 0.7373 (tpp-160) REVERT: M 68 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6994 (mm-30) REVERT: M 72 ASP cc_start: 0.8440 (m-30) cc_final: 0.8103 (m-30) REVERT: M 91 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7251 (tm-30) REVERT: M 187 ASP cc_start: 0.8089 (m-30) cc_final: 0.7854 (m-30) REVERT: N 84 MET cc_start: 0.5747 (mmm) cc_final: 0.5008 (tpt) REVERT: N 176 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7800 (tp30) outliers start: 56 outliers final: 24 residues processed: 249 average time/residue: 0.8397 time to fit residues: 226.9344 Evaluate side-chains 230 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 111 LYS Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Chi-restraints excluded: chain N residue 284 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN J 30 GLN L 62 ASN M 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087064 restraints weight = 24831.245| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.94 r_work: 0.3090 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16910 Z= 0.219 Angle : 0.567 8.889 22967 Z= 0.306 Chirality : 0.044 0.155 2599 Planarity : 0.005 0.044 2825 Dihedral : 13.373 87.630 2827 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.27 % Allowed : 22.16 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1995 helix: 1.21 (0.18), residues: 840 sheet: 0.77 (0.28), residues: 331 loop : -0.55 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 2 TYR 0.017 0.002 TYR L 315 PHE 0.017 0.002 PHE F 20 TRP 0.005 0.001 TRP O 9 HIS 0.005 0.001 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00514 (16910) covalent geometry : angle 0.56695 (22967) hydrogen bonds : bond 0.05028 ( 827) hydrogen bonds : angle 4.78492 ( 2262) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 205 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: O 5 PHE cc_start: 0.8021 (m-80) cc_final: 0.7548 (m-80) REVERT: O 36 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6582 (tptp) REVERT: O 70 ILE cc_start: 0.8373 (tp) cc_final: 0.7748 (pt) REVERT: O 71 GLU cc_start: 0.8217 (tt0) cc_final: 0.8007 (tm-30) REVERT: I 26 SER cc_start: 0.8001 (OUTLIER) cc_final: 0.7501 (p) REVERT: I 80 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8483 (mtpt) REVERT: I 181 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8079 (p) REVERT: I 306 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6852 (ptm-80) REVERT: I 326 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8790 (ttm) REVERT: J 27 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7542 (mmm-85) REVERT: K 306 ARG cc_start: 0.8111 (mmt90) cc_final: 0.7807 (mmp-170) REVERT: L 61 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8068 (mp) REVERT: L 70 LYS cc_start: 0.8304 (mmtp) cc_final: 0.8099 (mmtm) REVERT: L 213 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: M 26 SER cc_start: 0.8425 (m) cc_final: 0.8015 (p) REVERT: M 68 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6821 (mm-30) REVERT: M 72 ASP cc_start: 0.8426 (m-30) cc_final: 0.8005 (m-30) REVERT: M 91 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7361 (tm-30) REVERT: M 187 ASP cc_start: 0.8057 (m-30) cc_final: 0.7797 (m-30) REVERT: N 84 MET cc_start: 0.5828 (mmm) cc_final: 0.5032 (tpt) REVERT: N 176 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7824 (tp30) outliers start: 70 outliers final: 29 residues processed: 257 average time/residue: 0.8629 time to fit residues: 239.7221 Evaluate side-chains 238 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain I residue 181 SER Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 306 ARG Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 336 ASP Chi-restraints excluded: chain N residue 23 GLN Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Chi-restraints excluded: chain N residue 284 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 144 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN J 30 GLN L 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.088705 restraints weight = 24686.951| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.94 r_work: 0.3118 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16910 Z= 0.149 Angle : 0.509 8.830 22967 Z= 0.276 Chirality : 0.041 0.139 2599 Planarity : 0.004 0.041 2825 Dihedral : 13.298 89.368 2827 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.17 % Allowed : 23.57 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1995 helix: 1.38 (0.18), residues: 840 sheet: 0.48 (0.27), residues: 385 loop : -0.40 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 2 TYR 0.013 0.001 TYR L 315 PHE 0.015 0.001 PHE F 20 TRP 0.004 0.001 TRP O 9 HIS 0.003 0.001 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00338 (16910) covalent geometry : angle 0.50856 (22967) hydrogen bonds : bond 0.04121 ( 827) hydrogen bonds : angle 4.48942 ( 2262) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 0.648 Fit side-chains REVERT: O 5 PHE cc_start: 0.8011 (m-80) cc_final: 0.7637 (m-80) REVERT: O 70 ILE cc_start: 0.8253 (tp) cc_final: 0.7868 (pt) REVERT: I 26 SER cc_start: 0.7921 (OUTLIER) cc_final: 0.7432 (p) REVERT: I 184 ASP cc_start: 0.8129 (m-30) cc_final: 0.7745 (m-30) REVERT: I 306 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.6919 (ptm-80) REVERT: I 326 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8776 (ttm) REVERT: J 27 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7540 (mmm-85) REVERT: K 306 ARG cc_start: 0.8095 (mmt90) cc_final: 0.7798 (mmp-170) REVERT: L 61 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8112 (mp) REVERT: L 213 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: M 26 SER cc_start: 0.8398 (m) cc_final: 0.7959 (p) REVERT: M 27 ARG cc_start: 0.7340 (tpp-160) cc_final: 0.6858 (mpt90) REVERT: M 68 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: M 72 ASP cc_start: 0.8460 (m-30) cc_final: 0.8048 (m-30) REVERT: M 91 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7346 (tm-30) REVERT: M 187 ASP cc_start: 0.8051 (m-30) cc_final: 0.7744 (m-30) REVERT: M 247 ARG cc_start: 0.8496 (mtp-110) cc_final: 0.8212 (tpp-160) REVERT: N 84 MET cc_start: 0.5926 (mmm) cc_final: 0.5043 (tpt) REVERT: N 176 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7765 (tp30) outliers start: 52 outliers final: 24 residues processed: 249 average time/residue: 0.8455 time to fit residues: 228.2746 Evaluate side-chains 231 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 11 LYS Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 306 ARG Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 70 LYS Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 183 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 187 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN J 30 GLN L 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.115396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.086708 restraints weight = 24687.520| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.94 r_work: 0.3085 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16910 Z= 0.238 Angle : 0.580 8.864 22967 Z= 0.313 Chirality : 0.044 0.150 2599 Planarity : 0.005 0.050 2825 Dihedral : 13.425 87.612 2826 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.91 % Allowed : 22.95 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 1995 helix: 1.28 (0.18), residues: 834 sheet: 0.71 (0.28), residues: 331 loop : -0.63 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 3 TYR 0.017 0.002 TYR L 315 PHE 0.016 0.002 PHE F 20 TRP 0.003 0.001 TRP O 9 HIS 0.005 0.001 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00561 (16910) covalent geometry : angle 0.58028 (22967) hydrogen bonds : bond 0.05122 ( 827) hydrogen bonds : angle 4.75642 ( 2262) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: O 5 PHE cc_start: 0.7947 (m-80) cc_final: 0.7626 (m-80) REVERT: O 70 ILE cc_start: 0.8241 (tp) cc_final: 0.7875 (pt) REVERT: I 26 SER cc_start: 0.7958 (OUTLIER) cc_final: 0.7477 (p) REVERT: I 181 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8062 (p) REVERT: I 306 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6859 (ptm-80) REVERT: I 326 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8785 (ttm) REVERT: J 27 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7542 (mmm-85) REVERT: J 43 GLU cc_start: 0.8091 (pp20) cc_final: 0.7868 (pp20) REVERT: J 91 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8138 (mm-30) REVERT: K 306 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7821 (mmp-170) REVERT: L 61 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8101 (mp) REVERT: L 213 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: M 26 SER cc_start: 0.8417 (m) cc_final: 0.8009 (p) REVERT: M 68 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6826 (mm-30) REVERT: M 72 ASP cc_start: 0.8451 (m-30) cc_final: 0.8001 (m-30) REVERT: M 91 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7364 (tm-30) REVERT: M 187 ASP cc_start: 0.8024 (m-30) cc_final: 0.7752 (m-30) REVERT: M 206 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7722 (mp-120) REVERT: N 84 MET cc_start: 0.6098 (mmm) cc_final: 0.5114 (tpt) REVERT: N 176 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7834 (tp30) outliers start: 64 outliers final: 30 residues processed: 250 average time/residue: 0.8083 time to fit residues: 219.2486 Evaluate side-chains 238 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 181 SER Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 306 ARG Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 206 GLN Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 251 MET Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Chi-restraints excluded: chain N residue 284 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 139 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN J 30 GLN L 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.118339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.089820 restraints weight = 24617.841| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.94 r_work: 0.3133 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16910 Z= 0.119 Angle : 0.491 8.925 22967 Z= 0.266 Chirality : 0.040 0.136 2599 Planarity : 0.003 0.042 2825 Dihedral : 13.249 89.108 2826 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.38 % Allowed : 23.99 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 1995 helix: 1.48 (0.18), residues: 840 sheet: 0.48 (0.27), residues: 385 loop : -0.36 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 2 TYR 0.010 0.001 TYR K 315 PHE 0.013 0.001 PHE F 20 TRP 0.003 0.001 TRP O 9 HIS 0.002 0.000 HIS L 244 Details of bonding type rmsd covalent geometry : bond 0.00261 (16910) covalent geometry : angle 0.49054 (22967) hydrogen bonds : bond 0.03531 ( 827) hydrogen bonds : angle 4.32151 ( 2262) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.635 Fit side-chains REVERT: O 5 PHE cc_start: 0.7986 (m-80) cc_final: 0.7650 (m-80) REVERT: O 21 GLU cc_start: 0.7562 (mp0) cc_final: 0.7090 (pm20) REVERT: O 70 ILE cc_start: 0.8195 (tp) cc_final: 0.7881 (pt) REVERT: I 306 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7017 (ptm-80) REVERT: I 326 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8802 (ttm) REVERT: J 27 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7560 (mmm-85) REVERT: J 64 LYS cc_start: 0.7969 (tttm) cc_final: 0.7765 (ttmm) REVERT: K 95 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7798 (ttp80) REVERT: K 306 ARG cc_start: 0.8143 (mmt90) cc_final: 0.7803 (mmp-170) REVERT: L 61 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8143 (mp) REVERT: L 213 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: M 26 SER cc_start: 0.8339 (m) cc_final: 0.7903 (p) REVERT: M 27 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.6932 (mpt90) REVERT: M 68 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: M 72 ASP cc_start: 0.8474 (m-30) cc_final: 0.8066 (m-30) REVERT: M 91 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7380 (tm-30) REVERT: M 187 ASP cc_start: 0.8045 (m-30) cc_final: 0.7726 (m-30) REVERT: N 84 MET cc_start: 0.5968 (mmm) cc_final: 0.5030 (tpt) REVERT: N 176 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7771 (tp30) outliers start: 39 outliers final: 20 residues processed: 236 average time/residue: 0.8415 time to fit residues: 214.9688 Evaluate side-chains 229 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 306 ARG Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 251 MET Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Chi-restraints excluded: chain N residue 211 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 148 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN J 30 GLN K 94 GLN L 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.114605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086008 restraints weight = 24766.569| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.93 r_work: 0.3073 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 16910 Z= 0.303 Angle : 0.626 8.610 22967 Z= 0.337 Chirality : 0.047 0.161 2599 Planarity : 0.005 0.068 2825 Dihedral : 13.611 87.926 2826 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.05 % Allowed : 23.57 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.19), residues: 1995 helix: 1.21 (0.18), residues: 834 sheet: 0.67 (0.28), residues: 331 loop : -0.66 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 254 TYR 0.018 0.002 TYR L 315 PHE 0.018 0.002 PHE F 20 TRP 0.003 0.002 TRP O 20 HIS 0.006 0.001 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00717 (16910) covalent geometry : angle 0.62578 (22967) hydrogen bonds : bond 0.05670 ( 827) hydrogen bonds : angle 4.88444 ( 2262) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: O 5 PHE cc_start: 0.7901 (m-80) cc_final: 0.7599 (m-80) REVERT: O 70 ILE cc_start: 0.8214 (tp) cc_final: 0.7936 (pt) REVERT: I 26 SER cc_start: 0.8001 (OUTLIER) cc_final: 0.7531 (p) REVERT: I 181 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8095 (p) REVERT: J 27 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7562 (mmm-85) REVERT: J 64 LYS cc_start: 0.8024 (tttm) cc_final: 0.7811 (ttmm) REVERT: J 108 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: K 306 ARG cc_start: 0.8167 (mmt90) cc_final: 0.7860 (mmp-170) REVERT: L 61 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8127 (mp) REVERT: L 213 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: M 26 SER cc_start: 0.8494 (m) cc_final: 0.8072 (p) REVERT: M 68 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6877 (mm-30) REVERT: M 72 ASP cc_start: 0.8437 (m-30) cc_final: 0.7959 (m-30) REVERT: M 91 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7380 (tm-30) REVERT: M 206 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7552 (mp-120) REVERT: M 247 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8243 (tpp-160) REVERT: N 84 MET cc_start: 0.6149 (mmm) cc_final: 0.5126 (tpt) REVERT: N 176 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7834 (tp30) outliers start: 50 outliers final: 32 residues processed: 240 average time/residue: 0.8175 time to fit residues: 212.8849 Evaluate side-chains 232 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 181 SER Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 306 ARG Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 108 GLU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 339 ASP Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 206 GLN Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain N residue 324 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 166 optimal weight: 0.9990 chunk 146 optimal weight: 0.1980 chunk 191 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN J 30 GLN K 30 GLN L 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089402 restraints weight = 24637.624| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.22 r_work: 0.3112 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16910 Z= 0.128 Angle : 0.513 8.875 22967 Z= 0.276 Chirality : 0.040 0.136 2599 Planarity : 0.004 0.043 2825 Dihedral : 13.344 89.680 2826 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.50 % Allowed : 24.18 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1995 helix: 1.50 (0.18), residues: 834 sheet: 0.43 (0.27), residues: 385 loop : -0.46 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 2 TYR 0.011 0.001 TYR J 315 PHE 0.013 0.001 PHE F 20 TRP 0.002 0.001 TRP O 9 HIS 0.002 0.000 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00286 (16910) covalent geometry : angle 0.51328 (22967) hydrogen bonds : bond 0.03787 ( 827) hydrogen bonds : angle 4.40786 ( 2262) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.629 Fit side-chains REVERT: O 5 PHE cc_start: 0.7881 (m-80) cc_final: 0.7603 (m-80) REVERT: O 70 ILE cc_start: 0.8169 (tp) cc_final: 0.7846 (pt) REVERT: I 184 ASP cc_start: 0.8197 (m-30) cc_final: 0.7835 (m-30) REVERT: I 306 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6964 (ptm-80) REVERT: I 326 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8780 (ttm) REVERT: J 27 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7550 (mmm-85) REVERT: J 64 LYS cc_start: 0.7983 (tttm) cc_final: 0.7749 (ttmm) REVERT: K 95 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7796 (ttp80) REVERT: K 306 ARG cc_start: 0.8167 (mmt90) cc_final: 0.7824 (mmp-170) REVERT: L 61 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8159 (mp) REVERT: L 213 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: M 26 SER cc_start: 0.8386 (m) cc_final: 0.7936 (p) REVERT: M 68 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6807 (mm-30) REVERT: M 72 ASP cc_start: 0.8517 (m-30) cc_final: 0.8090 (m-30) REVERT: M 84 MET cc_start: 0.7931 (mtm) cc_final: 0.7727 (mtp) REVERT: M 91 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7404 (tm-30) REVERT: M 247 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8219 (tpp-160) REVERT: N 84 MET cc_start: 0.6032 (mmm) cc_final: 0.5058 (tpt) REVERT: N 176 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7821 (tp30) outliers start: 41 outliers final: 26 residues processed: 233 average time/residue: 0.8171 time to fit residues: 206.1110 Evaluate side-chains 231 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 10 CYS Chi-restraints excluded: chain O residue 11 LYS Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 306 ARG Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 64 LYS Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 90 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain N residue 324 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 153 optimal weight: 0.2980 chunk 166 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN J 30 GLN K 30 GLN L 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.118455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.089972 restraints weight = 24666.003| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.94 r_work: 0.3139 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16910 Z= 0.123 Angle : 0.505 9.529 22967 Z= 0.270 Chirality : 0.040 0.137 2599 Planarity : 0.004 0.043 2825 Dihedral : 13.183 87.173 2826 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.95 % Allowed : 24.91 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1995 helix: 1.55 (0.18), residues: 840 sheet: 0.47 (0.27), residues: 385 loop : -0.34 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 27 TYR 0.011 0.001 TYR L 315 PHE 0.013 0.001 PHE F 20 TRP 0.003 0.001 TRP O 20 HIS 0.003 0.000 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00274 (16910) covalent geometry : angle 0.50485 (22967) hydrogen bonds : bond 0.03537 ( 827) hydrogen bonds : angle 4.24646 ( 2262) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.707 Fit side-chains REVERT: O 21 GLU cc_start: 0.7519 (mp0) cc_final: 0.7269 (pm20) REVERT: O 70 ILE cc_start: 0.8155 (tp) cc_final: 0.7812 (pp) REVERT: I 184 ASP cc_start: 0.8136 (m-30) cc_final: 0.7784 (m-30) REVERT: I 326 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8784 (ttm) REVERT: J 27 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7594 (mmm-85) REVERT: J 64 LYS cc_start: 0.7947 (tttm) cc_final: 0.7713 (ttmm) REVERT: K 95 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7782 (ttp80) REVERT: K 210 MET cc_start: 0.8587 (mtm) cc_final: 0.8335 (mtp) REVERT: K 306 ARG cc_start: 0.8124 (mmt90) cc_final: 0.7816 (mmp-170) REVERT: L 184 ASP cc_start: 0.7856 (t0) cc_final: 0.7650 (t0) REVERT: M 26 SER cc_start: 0.8364 (m) cc_final: 0.7891 (p) REVERT: M 27 ARG cc_start: 0.7446 (tpp-160) cc_final: 0.6938 (mpt90) REVERT: M 68 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6826 (mm-30) REVERT: M 72 ASP cc_start: 0.8509 (m-30) cc_final: 0.8090 (m-30) REVERT: M 91 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7408 (tm-30) REVERT: N 84 MET cc_start: 0.6045 (mmm) cc_final: 0.5033 (tpt) REVERT: N 176 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7773 (tp30) outliers start: 32 outliers final: 23 residues processed: 236 average time/residue: 0.8263 time to fit residues: 211.0474 Evaluate side-chains 233 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 339 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain M residue 30 GLN Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Chi-restraints excluded: chain N residue 324 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 58 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 111 optimal weight: 0.0070 chunk 37 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 10 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN J 30 GLN K 30 GLN K 94 GLN L 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.089091 restraints weight = 24645.573| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.93 r_work: 0.3123 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16910 Z= 0.148 Angle : 0.528 8.782 22967 Z= 0.282 Chirality : 0.041 0.141 2599 Planarity : 0.004 0.042 2825 Dihedral : 13.224 88.026 2826 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.26 % Allowed : 24.91 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1995 helix: 1.50 (0.18), residues: 840 sheet: 0.45 (0.27), residues: 385 loop : -0.33 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 247 TYR 0.013 0.001 TYR L 315 PHE 0.013 0.001 PHE F 20 TRP 0.003 0.001 TRP O 9 HIS 0.003 0.001 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00339 (16910) covalent geometry : angle 0.52824 (22967) hydrogen bonds : bond 0.03935 ( 827) hydrogen bonds : angle 4.36182 ( 2262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7961.57 seconds wall clock time: 135 minutes 51.02 seconds (8151.02 seconds total)