Starting phenix.real_space_refine on Sat Jul 4 00:02:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9trm_56179/07_2026/9trm_56179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9trm_56179/07_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_56179/07_2026/9trm_56179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9trm_56179/07_2026/9trm_56179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9trm_56179/07_2026/9trm_56179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9trm_56179/07_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-dev-6108/lib/python3.11/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, 31 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 3.78, per 1000 atoms: 0.23 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: 1.01 Conformation dependent library (CDL) restraints added in 656.2 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: 1.74 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: 2.37 Time building geometry restraints manager: 1.46 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: 2148 0.052 - 0.105: 395 0.105 - 0.157: 52 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 3.250 nonbonded pdb=" O2B ATP K 401 " pdb="CA CA K 402 " model vdw 2.293 3.250 nonbonded pdb=" O2B ATP L 401 " pdb="CA CA L 402 " model vdw 2.336 3.250 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 3.250 ... (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: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.970 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:7.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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= 0.242 Angle : 0.627 14.256 22967 Z= 0.387 Chirality : 0.041 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/Z covalent geometry : bond 0.00382 / 0.24 (16910) covalent geometry : angle 0.62663 / 0.39 (22967) hydrogen bonds : bond 0.15923 / 12.86 ( 827) hydrogen bonds : angle 6.28502 / 6.94 ( 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 : 0.597 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: 0.7162 time to fit residues: 226.9153 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 : 0.588 ------------------------------------------------------------------------------- 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: 5.9990 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... ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN J 30 GLN K 30 GLN M 199 HIS N 200 GLN N 272 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.090752 restraints weight = 24403.751| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.95 r_work: 0.3154 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1324 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= 0.153 Angle : 0.545 8.158 22967 Z= 0.302 Chirality : 0.042 0.146 2599 Planarity : 0.004 0.038 2825 Dihedral : 12.977 83.500 2834 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.87 % Allowed : 22.95 % Favored : 74.18 % 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: 0.71 (0.19), residues: 1995 helix: 1.27 (0.18), residues: 840 sheet: 0.57 (0.27), residues: 385 loop : -0.38 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 27 TYR 0.018 0.001 TYR J 315 PHE 0.015 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/Z covalent geometry : bond 0.00326 / 0.15 (16910) covalent geometry : angle 0.54519 / 0.30 (22967) hydrogen bonds : bond 0.04693 / 3.81 ( 827) hydrogen bonds : angle 5.03074 / 5.67 ( 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 264 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 0.451 Fit side-chains REVERT: O 36 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6684 (tptp) REVERT: O 69 GLU cc_start: 0.8381 (tp30) cc_final: 0.7889 (mt-10) REVERT: O 71 GLU cc_start: 0.8256 (tt0) cc_final: 0.7970 (tm-30) REVERT: I 26 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7287 (p) REVERT: I 184 ASP cc_start: 0.8140 (m-30) cc_final: 0.7762 (m-30) REVERT: J 57 LYS cc_start: 0.8692 (tttm) cc_final: 0.8483 (ttpt) REVERT: L 62 ASN cc_start: 0.8557 (m-40) cc_final: 0.8317 (m110) REVERT: M 27 ARG cc_start: 0.7582 (mpt90) cc_final: 0.7380 (tpp-160) REVERT: M 68 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: N 84 MET cc_start: 0.5737 (mmm) cc_final: 0.5070 (tpt) REVERT: N 176 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7734 (tp30) outliers start: 47 outliers final: 11 residues processed: 248 average time/residue: 0.6845 time to fit residues: 184.4594 Evaluate side-chains 213 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain I residue 26 SER 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 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 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 211 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 199 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN I 30 GLN J 30 GLN N 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.118473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090199 restraints weight = 24823.457| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.93 r_work: 0.3147 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16910 Z= 0.149 Angle : 0.519 9.025 22967 Z= 0.287 Chirality : 0.042 0.149 2599 Planarity : 0.004 0.046 2825 Dihedral : 13.010 82.550 2827 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.38 % Allowed : 22.95 % Favored : 74.66 % 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: 0.79 (0.19), residues: 1995 helix: 1.37 (0.18), residues: 840 sheet: 0.62 (0.27), residues: 385 loop : -0.38 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 27 TYR 0.016 0.001 TYR J 315 PHE 0.014 0.001 PHE F 20 TRP 0.002 0.001 TRP O 9 HIS 0.003 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (16910) covalent geometry : angle 0.51940 / 0.29 (22967) hydrogen bonds : bond 0.04290 / 3.52 ( 827) hydrogen bonds : angle 4.71654 / 5.31 ( 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 252 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.571 Fit side-chains REVERT: O 36 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6676 (tptp) REVERT: I 39 LYS cc_start: 0.8443 (mtpm) cc_final: 0.8004 (mmmt) REVERT: I 184 ASP cc_start: 0.8200 (m-30) cc_final: 0.7817 (m-30) REVERT: I 326 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8801 (ttm) REVERT: K 306 ARG cc_start: 0.8388 (ttp-110) cc_final: 0.8117 (mmt90) REVERT: L 61 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8147 (mp) REVERT: L 62 ASN cc_start: 0.8537 (m-40) cc_final: 0.8286 (m110) REVERT: L 213 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: M 68 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7068 (mm-30) REVERT: M 72 ASP cc_start: 0.8532 (m-30) cc_final: 0.8209 (m-30) REVERT: M 91 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7269 (tm-30) REVERT: M 187 ASP cc_start: 0.8039 (m-30) cc_final: 0.7824 (m-30) REVERT: N 84 MET cc_start: 0.5770 (mmm) cc_final: 0.5079 (tpt) REVERT: N 176 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7769 (tp30) outliers start: 39 outliers final: 18 residues processed: 241 average time/residue: 0.6492 time to fit residues: 170.5622 Evaluate side-chains 227 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 36 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 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 87 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN I 30 GLN J 30 GLN K 30 GLN M 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.114468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.086787 restraints weight = 24851.767| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.88 r_work: 0.3086 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16910 Z= 0.292 Angle : 0.652 9.320 22967 Z= 0.356 Chirality : 0.048 0.181 2599 Planarity : 0.005 0.071 2825 Dihedral : 13.254 89.209 2827 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.91 % Allowed : 22.89 % Favored : 73.20 % 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: 0.44 (0.19), residues: 1995 helix: 1.02 (0.18), residues: 846 sheet: 0.41 (0.26), residues: 385 loop : -0.49 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 27 TYR 0.022 0.002 TYR L 315 PHE 0.016 0.002 PHE M 126 TRP 0.003 0.002 TRP O 20 HIS 0.007 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.29 (16910) covalent geometry : angle 0.65195 / 0.36 (22967) hydrogen bonds : bond 0.05960 / 4.92 ( 827) hydrogen bonds : angle 5.06429 / 5.63 ( 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 262 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 198 time to evaluate : 0.698 Fit side-chains REVERT: O 5 PHE cc_start: 0.7883 (m-80) cc_final: 0.7559 (m-80) REVERT: O 36 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6601 (tptp) REVERT: O 70 ILE cc_start: 0.8369 (tp) cc_final: 0.7744 (pt) REVERT: O 71 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8028 (tm-30) REVERT: I 39 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8028 (mmmt) REVERT: I 184 ASP cc_start: 0.8139 (m-30) cc_final: 0.7733 (m-30) REVERT: L 61 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8124 (mp) REVERT: L 62 ASN cc_start: 0.8507 (m-40) cc_final: 0.8257 (m110) REVERT: L 213 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: M 68 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6966 (mm-30) REVERT: M 72 ASP cc_start: 0.8452 (m-30) cc_final: 0.8078 (m-30) REVERT: M 91 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7348 (tm-30) REVERT: M 187 ASP cc_start: 0.8081 (m-30) cc_final: 0.7872 (m-30) REVERT: M 247 ARG cc_start: 0.8514 (mtp-110) cc_final: 0.8160 (tpp-160) REVERT: M 251 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8605 (mtt) REVERT: N 27 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6946 (mpt180) REVERT: N 84 MET cc_start: 0.5874 (mmm) cc_final: 0.5090 (tpt) REVERT: N 163 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: N 176 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7813 (tp30) outliers start: 64 outliers final: 28 residues processed: 246 average time/residue: 0.6979 time to fit residues: 186.4317 Evaluate side-chains 227 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 230 THR 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 K residue 233 SER Chi-restraints excluded: chain K residue 274 ASP 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 201 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 M residue 251 MET Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 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 163 GLU 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: 1.9990 chunk 43 optimal weight: 0.7980 chunk 198 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN I 30 GLN J 30 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.089561 restraints weight = 24664.780| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.88 r_work: 0.3130 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2004 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= 0.137 Angle : 0.522 8.767 22967 Z= 0.288 Chirality : 0.042 0.147 2599 Planarity : 0.004 0.040 2825 Dihedral : 13.254 85.834 2826 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.17 % Allowed : 23.50 % 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: 0.70 (0.19), residues: 1995 helix: 1.28 (0.18), residues: 846 sheet: 0.50 (0.27), residues: 385 loop : -0.40 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 27 TYR 0.014 0.001 TYR L 315 PHE 0.015 0.001 PHE F 20 TRP 0.002 0.001 TRP O 20 HIS 0.002 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (16910) covalent geometry : angle 0.52158 / 0.29 (22967) hydrogen bonds : bond 0.04258 / 3.51 ( 827) hydrogen bonds : angle 4.61141 / 5.15 ( 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 260 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.656 Fit side-chains REVERT: O 5 PHE cc_start: 0.7897 (m-80) cc_final: 0.7594 (m-80) REVERT: O 21 GLU cc_start: 0.7710 (mp0) cc_final: 0.7092 (pm20) REVERT: O 70 ILE cc_start: 0.8380 (tp) cc_final: 0.7683 (pt) REVERT: I 26 SER cc_start: 0.7977 (OUTLIER) cc_final: 0.7461 (p) REVERT: I 184 ASP cc_start: 0.8112 (m-30) cc_final: 0.7719 (m-30) REVERT: I 306 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6967 (ptm-80) REVERT: I 326 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8796 (ttm) REVERT: J 27 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7556 (mmm-85) REVERT: L 61 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8147 (mp) REVERT: L 62 ASN cc_start: 0.8503 (m-40) cc_final: 0.8238 (m110) REVERT: L 70 LYS cc_start: 0.8316 (mmtp) cc_final: 0.8114 (mmtm) REVERT: L 213 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: M 26 SER cc_start: 0.8472 (m) cc_final: 0.8034 (p) REVERT: M 68 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6906 (mm-30) REVERT: M 72 ASP cc_start: 0.8474 (m-30) cc_final: 0.8065 (m-30) REVERT: M 91 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7368 (tm-30) REVERT: M 187 ASP cc_start: 0.7998 (m-30) cc_final: 0.7729 (m-30) REVERT: M 247 ARG cc_start: 0.8468 (mtp-110) cc_final: 0.8149 (tpp-160) REVERT: N 27 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6809 (mpt180) REVERT: N 84 MET cc_start: 0.5801 (mmm) cc_final: 0.5041 (tpt) REVERT: N 163 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: N 176 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7818 (tp30) REVERT: N 202 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7646 (mp-120) outliers start: 52 outliers final: 20 residues processed: 247 average time/residue: 0.6565 time to fit residues: 176.7600 Evaluate side-chains 230 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 72 VAL 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 104 THR Chi-restraints excluded: chain J residue 251 MET 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 26 SER Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 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 M residue 330 ASN Chi-restraints excluded: chain N residue 23 GLN Chi-restraints excluded: chain N residue 27 ARG 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 163 GLU 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: 7.9990 chunk 205 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN I 30 GLN J 30 GLN K 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.087149 restraints weight = 24566.182| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.93 r_work: 0.3093 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16910 Z= 0.224 Angle : 0.577 8.567 22967 Z= 0.317 Chirality : 0.045 0.168 2599 Planarity : 0.005 0.049 2825 Dihedral : 13.270 88.088 2826 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.36 % Allowed : 23.38 % 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: 0.60 (0.19), residues: 1995 helix: 1.24 (0.18), residues: 840 sheet: 0.75 (0.28), residues: 331 loop : -0.59 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 2 TYR 0.017 0.002 TYR L 315 PHE 0.016 0.002 PHE F 20 TRP 0.002 0.001 TRP O 20 HIS 0.005 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (16910) covalent geometry : angle 0.57716 / 0.32 (22967) hydrogen bonds : bond 0.05075 / 4.20 ( 827) hydrogen bonds : angle 4.78022 / 5.34 ( 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 256 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 0.558 Fit side-chains REVERT: O 5 PHE cc_start: 0.7904 (m-80) cc_final: 0.7596 (m-80) REVERT: O 70 ILE cc_start: 0.8324 (tp) cc_final: 0.7885 (pt) REVERT: I 26 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7509 (p) REVERT: I 184 ASP cc_start: 0.8130 (m-30) cc_final: 0.7720 (m-30) REVERT: I 306 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6947 (ptm-80) REVERT: J 27 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7531 (mmm-85) REVERT: L 61 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8085 (mp) REVERT: L 62 ASN cc_start: 0.8474 (m-40) cc_final: 0.8266 (m110) REVERT: L 213 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: M 26 SER cc_start: 0.8427 (m) cc_final: 0.8018 (p) REVERT: M 68 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6826 (mm-30) REVERT: M 72 ASP cc_start: 0.8450 (m-30) cc_final: 0.7993 (m-30) REVERT: M 91 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7339 (tm-30) REVERT: M 187 ASP cc_start: 0.7981 (m-30) cc_final: 0.7680 (m-30) REVERT: N 27 ARG cc_start: 0.7044 (mpt180) cc_final: 0.6793 (mpt180) REVERT: N 84 MET cc_start: 0.5844 (mmm) cc_final: 0.5044 (tpt) REVERT: N 163 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8433 (mt-10) REVERT: N 176 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7834 (tp30) outliers start: 55 outliers final: 28 residues processed: 238 average time/residue: 0.6538 time to fit residues: 169.3752 Evaluate side-chains 231 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 230 THR Chi-restraints excluded: chain I residue 306 ARG Chi-restraints excluded: chain J residue 61 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 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 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 163 GLU Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 139 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN I 30 GLN J 30 GLN K 30 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.088611 restraints weight = 24441.389| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.93 r_work: 0.3117 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16910 Z= 0.149 Angle : 0.525 8.938 22967 Z= 0.289 Chirality : 0.042 0.147 2599 Planarity : 0.004 0.055 2825 Dihedral : 13.294 85.327 2826 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.87 % Allowed : 23.87 % 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: 0.71 (0.19), residues: 1995 helix: 1.33 (0.18), residues: 846 sheet: 0.46 (0.27), residues: 385 loop : -0.41 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 306 TYR 0.013 0.001 TYR L 315 PHE 0.015 0.001 PHE F 20 TRP 0.002 0.001 TRP O 9 HIS 0.003 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16910) covalent geometry : angle 0.52537 / 0.29 (22967) hydrogen bonds : bond 0.04235 / 3.50 ( 827) hydrogen bonds : angle 4.53500 / 5.07 ( 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 250 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.607 Fit side-chains REVERT: O 5 PHE cc_start: 0.7876 (m-80) cc_final: 0.7579 (m-80) REVERT: O 21 GLU cc_start: 0.7690 (mp0) cc_final: 0.7128 (pm20) REVERT: O 70 ILE cc_start: 0.8238 (tp) cc_final: 0.7877 (pt) REVERT: I 26 SER cc_start: 0.7925 (OUTLIER) cc_final: 0.7436 (p) REVERT: I 306 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6970 (ptm-80) REVERT: J 27 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7543 (mmm-85) REVERT: K 306 ARG cc_start: 0.8434 (ttp-110) cc_final: 0.8144 (tpp-160) REVERT: L 61 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8071 (mp) REVERT: L 62 ASN cc_start: 0.8445 (m-40) cc_final: 0.8194 (m110) REVERT: L 70 LYS cc_start: 0.8294 (mmtp) cc_final: 0.8093 (mmtm) REVERT: L 213 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: M 26 SER cc_start: 0.8367 (m) cc_final: 0.7925 (p) REVERT: M 68 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6830 (mm-30) REVERT: M 72 ASP cc_start: 0.8470 (m-30) cc_final: 0.8045 (m-30) REVERT: M 91 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7323 (tm-30) REVERT: M 187 ASP cc_start: 0.7969 (m-30) cc_final: 0.7640 (m-30) REVERT: M 247 ARG cc_start: 0.8506 (mtp-110) cc_final: 0.8198 (tpp-160) REVERT: N 57 LYS cc_start: 0.8064 (tttt) cc_final: 0.7679 (mptt) REVERT: N 84 MET cc_start: 0.5891 (mmm) cc_final: 0.5052 (tpt) REVERT: N 163 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: N 176 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7782 (tp30) outliers start: 47 outliers final: 27 residues processed: 238 average time/residue: 0.7143 time to fit residues: 184.9316 Evaluate side-chains 232 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 109 LEU Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 251 MET 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 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 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 134 THR Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 163 GLU Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 148 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN I 30 GLN J 30 GLN K 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.114498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.085779 restraints weight = 24694.284| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.93 r_work: 0.3070 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 16910 Z= 0.312 Angle : 0.655 8.986 22967 Z= 0.358 Chirality : 0.048 0.183 2599 Planarity : 0.005 0.075 2825 Dihedral : 13.472 89.617 2826 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.87 % Allowed : 23.81 % 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: 0.37 (0.19), residues: 1995 helix: 1.07 (0.18), residues: 840 sheet: 0.61 (0.28), residues: 331 loop : -0.72 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 306 TYR 0.019 0.002 TYR L 315 PHE 0.017 0.002 PHE F 20 TRP 0.003 0.002 TRP O 20 HIS 0.007 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.31 (16910) covalent geometry : angle 0.65479 / 0.36 (22967) hydrogen bonds : bond 0.05905 / 4.88 ( 827) hydrogen bonds : angle 4.98957 / 5.55 ( 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 247 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.419 Fit side-chains REVERT: O 5 PHE cc_start: 0.7901 (m-80) cc_final: 0.7609 (m-80) REVERT: O 70 ILE cc_start: 0.8285 (tp) cc_final: 0.7920 (pt) REVERT: I 26 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7576 (p) REVERT: I 181 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8125 (p) REVERT: I 306 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6919 (ptm-80) REVERT: J 27 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7553 (mmm-85) REVERT: J 91 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8154 (mm-30) REVERT: L 61 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8070 (mp) REVERT: L 62 ASN cc_start: 0.8487 (m-40) cc_final: 0.8269 (m110) REVERT: L 213 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: M 68 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6827 (mm-30) REVERT: M 72 ASP cc_start: 0.8430 (m-30) cc_final: 0.7952 (m-30) REVERT: M 91 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7371 (tm-30) REVERT: M 187 ASP cc_start: 0.8002 (m-30) cc_final: 0.7716 (m-30) REVERT: N 84 MET cc_start: 0.6150 (mmm) cc_final: 0.5174 (tpt) REVERT: N 163 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8492 (mt-10) REVERT: N 176 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7832 (tp30) outliers start: 47 outliers final: 27 residues processed: 236 average time/residue: 0.6722 time to fit residues: 172.6930 Evaluate side-chains 233 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 197 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 109 LEU Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 251 MET 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 61 ILE Chi-restraints excluded: chain L residue 87 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 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 23 GLN Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 163 GLU Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN 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: 6.9990 chunk 191 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN I 30 GLN J 30 GLN K 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.089068 restraints weight = 24508.128| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.94 r_work: 0.3124 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16910 Z= 0.133 Angle : 0.531 9.151 22967 Z= 0.291 Chirality : 0.041 0.155 2599 Planarity : 0.004 0.058 2825 Dihedral : 13.416 84.658 2826 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.14 % Allowed : 24.91 % Favored : 72.95 % 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: 0.65 (0.19), residues: 1995 helix: 1.35 (0.18), residues: 840 sheet: 0.70 (0.28), residues: 331 loop : -0.60 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 306 TYR 0.010 0.001 TYR K 315 PHE 0.014 0.001 PHE F 20 TRP 0.001 0.001 TRP O 20 HIS 0.002 0.000 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (16910) covalent geometry : angle 0.53053 / 0.29 (22967) hydrogen bonds : bond 0.04035 / 3.32 ( 827) hydrogen bonds : angle 4.50094 / 5.03 ( 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 240 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.675 Fit side-chains REVERT: O 5 PHE cc_start: 0.7846 (m-80) cc_final: 0.7549 (m-80) REVERT: O 21 GLU cc_start: 0.7647 (mp0) cc_final: 0.7387 (pm20) REVERT: O 70 ILE cc_start: 0.8193 (tp) cc_final: 0.7873 (pt) REVERT: I 306 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7033 (ptm-80) REVERT: J 27 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7520 (mmm-85) REVERT: K 306 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.8132 (tpp-160) REVERT: L 61 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.8072 (mp) REVERT: L 62 ASN cc_start: 0.8421 (m-40) cc_final: 0.8203 (m110) REVERT: L 70 LYS cc_start: 0.8291 (mmtp) cc_final: 0.8089 (mmtm) REVERT: L 213 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: M 26 SER cc_start: 0.8352 (m) cc_final: 0.7895 (p) REVERT: M 27 ARG cc_start: 0.7425 (tpp-160) cc_final: 0.6911 (mtt90) REVERT: M 68 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6903 (mm-30) REVERT: M 72 ASP cc_start: 0.8435 (m-30) cc_final: 0.8020 (m-30) REVERT: M 91 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7365 (tm-30) REVERT: M 187 ASP cc_start: 0.7970 (m-30) cc_final: 0.7633 (m-30) REVERT: M 247 ARG cc_start: 0.8495 (mtp-110) cc_final: 0.8197 (tpp-160) REVERT: N 84 MET cc_start: 0.5944 (mmm) cc_final: 0.5038 (tpt) REVERT: N 163 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8464 (mt-10) REVERT: N 176 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7780 (tp30) outliers start: 35 outliers final: 24 residues processed: 232 average time/residue: 0.7562 time to fit residues: 191.2526 Evaluate side-chains 234 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 251 MET Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 251 MET 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 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 23 GLN Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 163 GLU Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN I 30 GLN J 30 GLN K 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.086888 restraints weight = 24568.728| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.93 r_work: 0.3089 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 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 : 0.005 0.043 16910 Z= 0.232 Angle : 0.598 8.856 22967 Z= 0.327 Chirality : 0.045 0.172 2599 Planarity : 0.005 0.061 2825 Dihedral : 13.430 88.163 2826 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.01 % Allowed : 25.09 % Favored : 72.89 % 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: 0.54 (0.19), residues: 1995 helix: 1.26 (0.18), residues: 840 sheet: 0.65 (0.28), residues: 331 loop : -0.65 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 306 TYR 0.017 0.002 TYR L 315 PHE 0.017 0.002 PHE F 20 TRP 0.002 0.001 TRP O 20 HIS 0.005 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (16910) covalent geometry : angle 0.59789 / 0.33 (22967) hydrogen bonds : bond 0.05118 / 4.23 ( 827) hydrogen bonds : angle 4.75572 / 5.30 ( 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 236 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.655 Fit side-chains REVERT: O 5 PHE cc_start: 0.7892 (m-80) cc_final: 0.7597 (m-80) REVERT: O 21 GLU cc_start: 0.7645 (mp0) cc_final: 0.7169 (pm20) REVERT: O 70 ILE cc_start: 0.8212 (tp) cc_final: 0.7891 (pt) REVERT: I 184 ASP cc_start: 0.8240 (m-30) cc_final: 0.7904 (m-30) REVERT: I 306 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6923 (ptm-80) REVERT: J 27 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7541 (mmm-85) REVERT: J 64 LYS cc_start: 0.8013 (tttm) cc_final: 0.7796 (ttmm) REVERT: K 306 ARG cc_start: 0.8444 (ttp-110) cc_final: 0.8171 (tpp-160) REVERT: L 61 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8073 (mp) REVERT: L 62 ASN cc_start: 0.8435 (m-40) cc_final: 0.8223 (m110) REVERT: L 213 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: M 26 SER cc_start: 0.8399 (m) cc_final: 0.7940 (p) REVERT: M 68 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6873 (mm-30) REVERT: M 72 ASP cc_start: 0.8423 (m-30) cc_final: 0.7974 (m-30) REVERT: M 91 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7360 (tm-30) REVERT: M 247 ARG cc_start: 0.8485 (mtp-110) cc_final: 0.8223 (tpp-160) REVERT: N 84 MET cc_start: 0.6050 (mmm) cc_final: 0.5065 (tpt) REVERT: N 163 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8510 (mt-10) REVERT: N 176 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7797 (tp30) outliers start: 33 outliers final: 24 residues processed: 228 average time/residue: 0.7509 time to fit residues: 186.5797 Evaluate side-chains 230 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 251 MET Chi-restraints excluded: chain K residue 61 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 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 23 GLN Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 163 GLU Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 58 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 111 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN I 30 GLN J 30 GLN K 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089235 restraints weight = 24504.519| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.94 r_work: 0.3126 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16910 Z= 0.129 Angle : 0.526 8.919 22967 Z= 0.289 Chirality : 0.041 0.152 2599 Planarity : 0.004 0.057 2825 Dihedral : 13.411 83.708 2826 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.26 % Allowed : 25.27 % Favored : 72.47 % 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: 0.72 (0.19), residues: 1995 helix: 1.41 (0.18), residues: 840 sheet: 0.74 (0.28), residues: 331 loop : -0.55 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 306 TYR 0.011 0.001 TYR J 315 PHE 0.014 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/Z covalent geometry : bond 0.00270 / 0.13 (16910) covalent geometry : angle 0.52600 / 0.29 (22967) hydrogen bonds : bond 0.03957 / 3.26 ( 827) hydrogen bonds : angle 4.45426 / 4.98 ( 2262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6659.46 seconds wall clock time: 113 minutes 42.03 seconds (6822.03 seconds total)