Starting phenix.real_space_refine on Thu Aug 6 19:50:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9trm_56179/08_2026/9trm_56179.cif Found real_map, /net/cci-nas-00/data/ceres_data/9trm_56179/08_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_56179/08_2026/9trm_56179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9trm_56179/08_2026/9trm_56179.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9trm_56179/08_2026/9trm_56179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9trm_56179/08_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.66, per 1000 atoms: 0.22 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: 1.48 Conformation dependent library (CDL) restraints added in 741.3 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: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Proline residue: A 7 - end of helix Processing helix chain 'B' and resid 2 through 10 removed outlier: 3.745A pdb=" N ALA B 6 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Proline residue: B 7 - end of helix removed outlier: 3.537A pdb=" N LEU B 10 " --> pdb=" O PRO B 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Proline residue: E 7 - end of helix Processing helix chain 'C' and resid 2 through 10 Proline residue: C 7 - end of helix Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'I' and resid 24 through 31 Processing helix chain 'I' and resid 34 through 43 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 56 through 62 Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.567A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 98 removed outlier: 3.754A pdb=" N GLU I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 132 through 144 removed outlier: 3.595A pdb=" N VAL I 142 " --> pdb=" O HIS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.872A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 196 through 214 removed outlier: 3.907A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN I 206 " --> pdb=" O GLN I 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 232 removed outlier: 4.027A pdb=" N THR I 230 " --> pdb=" O ALA I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 237 through 260 Processing helix chain 'I' and resid 288 through 296 removed outlier: 3.723A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 32 removed outlier: 3.817A pdb=" N GLN J 30 " --> pdb=" O SER J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 45 Processing helix chain 'J' and resid 48 through 55 Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'J' and resid 67 through 80 Processing helix chain 'J' and resid 89 through 98 removed outlier: 4.179A pdb=" N GLU J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 113 Processing helix chain 'J' and resid 132 through 144 removed outlier: 3.620A pdb=" N VAL J 142 " --> pdb=" O HIS J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 178 removed outlier: 3.828A pdb=" N LEU J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 188 Processing helix chain 'J' and resid 196 through 212 removed outlier: 3.987A pdb=" N LEU J 204 " --> pdb=" O GLN J 200 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR J 205 " --> pdb=" O THR J 201 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN J 206 " --> pdb=" O GLN J 202 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA J 209 " --> pdb=" O TYR J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 232 removed outlier: 3.998A pdb=" N THR J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 237 through 260 Processing helix chain 'J' and resid 288 through 296 removed outlier: 3.673A pdb=" N ILE J 292 " --> pdb=" O GLY J 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 32 removed outlier: 3.678A pdb=" N GLY K 32 " --> pdb=" O GLU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 55 Processing helix chain 'K' and resid 56 through 62 removed outlier: 3.545A pdb=" N ASN K 62 " --> pdb=" O LYS K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.559A pdb=" N LEU K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 97 Processing helix chain 'K' and resid 106 through 114 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.598A pdb=" N VAL K 142 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 178 removed outlier: 3.733A pdb=" N LEU K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 214 removed outlier: 3.778A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 232 removed outlier: 3.951A pdb=" N THR K 230 " --> pdb=" O ALA K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 236 No H-bonds generated for 'chain 'K' and resid 234 through 236' Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 288 through 296 removed outlier: 3.727A pdb=" N ILE K 292 " --> pdb=" O GLY K 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 30 Processing helix chain 'L' and resid 34 through 44 Processing helix chain 'L' and resid 48 through 55 Processing helix chain 'L' and resid 56 through 63 removed outlier: 3.775A pdb=" N ILE L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 Processing helix chain 'L' and resid 89 through 97 Processing helix chain 'L' and resid 106 through 114 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.523A pdb=" N VAL L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 146 No H-bonds generated for 'chain 'L' and resid 145 through 146' Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 179 removed outlier: 3.829A pdb=" N LEU L 171 " --> pdb=" O ARG L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 214 removed outlier: 4.010A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA L 209 " --> pdb=" O TYR L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 232 removed outlier: 3.923A pdb=" N THR L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 236 No H-bonds generated for 'chain 'L' and resid 234 through 236' Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 288 through 296 removed outlier: 3.618A pdb=" N ILE L 292 " --> pdb=" O GLY L 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 31 removed outlier: 3.547A pdb=" N GLN M 30 " --> pdb=" O SER M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 44 removed outlier: 3.628A pdb=" N ALA M 44 " --> pdb=" O LYS M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 54 Processing helix chain 'M' and resid 56 through 63 removed outlier: 3.810A pdb=" N LEU M 60 " --> pdb=" O PRO M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 82 Processing helix chain 'M' and resid 89 through 97 Processing helix chain 'M' and resid 107 through 113 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.520A pdb=" N VAL M 142 " --> pdb=" O HIS M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 179 removed outlier: 3.865A pdb=" N LEU M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 214 removed outlier: 3.974A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 232 removed outlier: 3.514A pdb=" N TYR M 232 " --> pdb=" O TYR M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 288 through 296 removed outlier: 3.832A pdb=" N ILE M 292 " --> pdb=" O GLY M 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 32 removed outlier: 4.043A pdb=" N GLU N 29 " --> pdb=" O ILE N 25 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN N 30 " --> pdb=" O SER N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 45 Processing helix chain 'N' and resid 48 through 54 Processing helix chain 'N' and resid 56 through 63 removed outlier: 3.596A pdb=" N LEU N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE N 63 " --> pdb=" O GLU N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 82 removed outlier: 3.673A pdb=" N LEU N 81 " --> pdb=" O GLU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 97 removed outlier: 3.716A pdb=" N PHE N 92 " --> pdb=" O THR N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 114 Processing helix chain 'N' and resid 132 through 144 Processing helix chain 'N' and resid 145 through 146 No H-bonds generated for 'chain 'N' and resid 145 through 146' Processing helix chain 'N' and resid 147 through 151 Processing helix chain 'N' and resid 167 through 178 removed outlier: 3.648A pdb=" N LEU N 171 " --> pdb=" O ARG N 167 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR N 178 " --> pdb=" O VAL N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 214 removed outlier: 3.644A pdb=" N THR N 201 " --> pdb=" O THR N 197 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA N 209 " --> pdb=" O TYR N 205 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL N 212 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER N 214 " --> pdb=" O MET N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 232 Processing helix chain 'N' and resid 234 through 236 No H-bonds generated for 'chain 'N' and resid 234 through 236' Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 288 through 294 removed outlier: 3.651A pdb=" N ILE N 292 " --> pdb=" O GLY N 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 42 through 44 removed outlier: 3.735A pdb=" N GLY O 44 " --> pdb=" O LEU O 35 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY O 22 " --> pdb=" O TRP O 9 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR O 4 " --> pdb=" O VAL O 75 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL O 75 " --> pdb=" O TYR O 4 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER O 6 " --> pdb=" O MET O 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 87 through 88 removed outlier: 6.615A pdb=" N ALA J 157 " --> pdb=" O ALA J 190 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ALA J 192 " --> pdb=" O ALA J 157 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR J 159 " --> pdb=" O ALA J 192 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS J 156 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU J 218 " --> pdb=" O LYS J 156 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA J 217 " --> pdb=" O ALA J 262 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL J 264 " --> pdb=" O ALA J 217 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU J 219 " --> pdb=" O VAL J 264 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR J 266 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL J 221 " --> pdb=" O THR J 266 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY J 127 " --> pdb=" O ASN J 267 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE J 122 " --> pdb=" O THR J 298 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU J 300 " --> pdb=" O ILE J 122 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU J 124 " --> pdb=" O LEU J 300 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU J 302 " --> pdb=" O GLU J 124 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE J 126 " --> pdb=" O LEU J 302 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N LYS J 304 " --> pdb=" O PHE J 126 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG J 299 " --> pdb=" O TYR J 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AA4, first strand: chain 'I' and resid 189 through 193 removed outlier: 6.679A pdb=" N LYS I 156 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ILE I 220 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET I 158 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASP I 222 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE I 160 " --> pdb=" O ASP I 222 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY I 333 " --> pdb=" O ASN I 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AA6, first strand: chain 'J' and resid 87 through 88 removed outlier: 5.546A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU K 218 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AA8, first strand: chain 'J' and resid 269 through 271 Processing sheet with id=AA9, first strand: chain 'K' and resid 87 through 88 removed outlier: 6.921A pdb=" N LYS L 156 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU L 219 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET L 158 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL L 221 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE L 160 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE L 122 " --> pdb=" O THR L 298 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU L 300 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU L 124 " --> pdb=" O LEU L 300 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU L 302 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE L 126 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N LYS L 304 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 101 through 102 Processing sheet with id=AB2, first strand: chain 'K' and resid 269 through 271 Processing sheet with id=AB3, first strand: chain 'L' and resid 87 through 88 removed outlier: 6.627A pdb=" N LYS M 156 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ILE M 220 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET M 158 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP M 222 " --> pdb=" O MET M 158 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE M 160 " --> pdb=" O ASP M 222 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 101 through 102 Processing sheet with id=AB5, first strand: chain 'L' and resid 269 through 271 Processing sheet with id=AB6, first strand: chain 'M' and resid 87 through 88 removed outlier: 6.688A pdb=" N ALA N 157 " --> pdb=" O ALA N 190 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ALA N 192 " --> pdb=" O ALA N 157 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR N 159 " --> pdb=" O ALA N 192 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS N 156 " --> pdb=" O TYR N 216 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU N 218 " --> pdb=" O LYS N 156 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY N 127 " --> pdb=" O ASN N 267 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 101 through 102 Processing sheet with id=AB8, first strand: chain 'M' and resid 269 through 271 Processing sheet with id=AB9, first strand: chain 'N' and resid 101 through 102 Processing sheet with id=AC1, first strand: chain 'N' and resid 269 through 271 788 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 1.92 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 2.510 nonbonded pdb=" O2B ATP K 401 " pdb="CA CA K 402 " model vdw 2.293 2.510 nonbonded pdb=" O2B ATP L 401 " pdb="CA CA L 402 " model vdw 2.336 2.510 nonbonded pdb=" O SER L 26 " pdb=" OE1 GLU L 29 " model vdw 2.352 3.040 nonbonded pdb=" O3G ATP M 401 " pdb="CA CA M 402 " model vdw 2.367 2.510 ... (remaining 135283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26)) selection = (chain 'C' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26)) selection = (chain 'D' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26)) selection = (chain 'E' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 26)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 21 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 112 or (resid 113 through 114 and \ (name N or name CA or name C or name O or name CB )) or resid 115 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 3 through 402)) selection = (chain 'J' and (resid 21 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 112 or (resid 113 through 114 and \ (name N or name CA or name C or name O or name CB )) or resid 115 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 3 through 402)) selection = (chain 'K' and (resid 21 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 112 or (resid 113 through 114 and \ (name N or name CA or name C or name O or name CB )) or resid 115 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 3 through 402)) selection = (chain 'L' and (resid 21 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 112 or (resid 113 through 114 and \ (name N or name CA or name C or name O or name CB )) or resid 115 through 331 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 3 through 402)) selection = (chain 'M' and (resid 21 through 112 or (resid 113 through 114 and (name N or na \ me CA or name C or name O or name CB )) or resid 115 through 331 or (resid 332 a \ nd (name N or name CA or name C or name O or name CB )) or resid 333 through 402 \ )) selection = (chain 'N' and (resid 21 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.370 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- 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= 0.388 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 0.62721 / 0.39 (22967) hydrogen bonds : bond 0.15923 / 12.88 ( 827) hydrogen bonds : angle 6.28502 / 6.95 ( 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 : 0.598 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: 0.8207 time to fit residues: 260.2008 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 : 0.809 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.119292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.090705 restraints weight = 24501.350| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.94 r_work: 0.3154 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1299 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= 0.153 Angle : 0.543 8.145 22967 Z= 0.301 Chirality : 0.042 0.152 2599 Planarity : 0.004 0.039 2825 Dihedral : 13.042 84.255 2834 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.75 % Allowed : 23.14 % Favored : 74.11 % 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: 0.58 (0.27), residues: 385 loop : -0.39 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 27 TYR 0.017 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 0.00325 / 0.15 (16910) covalent geometry : angle 0.54316 / 0.30 (22967) hydrogen bonds : bond 0.04680 / 3.82 ( 827) hydrogen bonds : angle 5.04249 / 5.70 ( 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 259 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.652 Fit side-chains REVERT: O 36 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6683 (tptp) REVERT: O 69 GLU cc_start: 0.8395 (tp30) cc_final: 0.7895 (mt-10) REVERT: O 71 GLU cc_start: 0.8254 (tt0) cc_final: 0.7958 (tm-30) REVERT: I 26 SER cc_start: 0.7850 (OUTLIER) cc_final: 0.7280 (p) REVERT: I 184 ASP cc_start: 0.8154 (m-30) cc_final: 0.7782 (m-30) REVERT: J 57 LYS cc_start: 0.8675 (tttm) cc_final: 0.8467 (ttpt) REVERT: K 306 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7975 (ttp-110) REVERT: L 62 ASN cc_start: 0.8557 (m-40) cc_final: 0.8342 (m110) REVERT: M 27 ARG cc_start: 0.7580 (mpt90) cc_final: 0.7379 (tpp-160) REVERT: N 84 MET cc_start: 0.5728 (mmm) cc_final: 0.5067 (tpt) REVERT: N 176 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7727 (tp30) outliers start: 45 outliers final: 11 residues processed: 244 average time/residue: 0.7574 time to fit residues: 200.7641 Evaluate side-chains 214 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 138 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.118351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.090196 restraints weight = 24771.749| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.92 r_work: 0.3147 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1599 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= 0.145 Angle : 0.515 8.686 22967 Z= 0.285 Chirality : 0.042 0.150 2599 Planarity : 0.004 0.051 2825 Dihedral : 13.121 86.558 2827 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.63 % Allowed : 22.22 % Favored : 75.15 % 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: 0.80 (0.19), residues: 1995 helix: 1.38 (0.18), residues: 840 sheet: 0.63 (0.27), residues: 385 loop : -0.39 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 27 TYR 0.016 0.001 TYR L 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 0.00314 / 0.14 (16910) covalent geometry : angle 0.51507 / 0.29 (22967) hydrogen bonds : bond 0.04244 / 3.50 ( 827) hydrogen bonds : angle 4.64462 / 5.23 ( 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 261 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.654 Fit side-chains REVERT: O 5 PHE cc_start: 0.7947 (m-80) cc_final: 0.7720 (m-80) REVERT: O 36 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6725 (tptp) REVERT: O 71 GLU cc_start: 0.8298 (tt0) cc_final: 0.8033 (tm-30) REVERT: I 39 LYS cc_start: 0.8447 (mtpm) cc_final: 0.8014 (mmmt) REVERT: I 184 ASP cc_start: 0.8169 (m-30) cc_final: 0.7793 (m-30) REVERT: I 326 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8811 (ttm) REVERT: K 306 ARG cc_start: 0.8178 (mmt90) cc_final: 0.7889 (mmp-170) REVERT: L 61 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8152 (mp) REVERT: L 62 ASN cc_start: 0.8569 (m-40) cc_final: 0.8288 (m110) REVERT: L 213 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: M 72 ASP cc_start: 0.8486 (m-30) cc_final: 0.8181 (m-30) REVERT: M 91 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7264 (tm-30) REVERT: N 84 MET cc_start: 0.5775 (mmm) cc_final: 0.5078 (tpt) REVERT: N 176 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7742 (tp30) outliers start: 43 outliers final: 19 residues processed: 249 average time/residue: 0.8039 time to fit residues: 217.9067 Evaluate side-chains 225 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Chi-restraints excluded: chain N residue 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: 0.9980 chunk 192 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.116571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.089034 restraints weight = 24811.720| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.89 r_work: 0.3123 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16910 Z= 0.184 Angle : 0.550 9.106 22967 Z= 0.302 Chirality : 0.043 0.156 2599 Planarity : 0.004 0.041 2825 Dihedral : 13.194 89.766 2827 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.93 % Allowed : 23.50 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1995 helix: 1.35 (0.18), residues: 840 sheet: 0.56 (0.26), residues: 385 loop : -0.41 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 2 TYR 0.017 0.001 TYR L 315 PHE 0.014 0.002 PHE F 20 TRP 0.004 0.001 TRP O 9 HIS 0.005 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (16910) covalent geometry : angle 0.54973 / 0.30 (22967) hydrogen bonds : bond 0.04666 / 3.85 ( 827) hydrogen bonds : angle 4.67952 / 5.22 ( 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 255 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.560 Fit side-chains REVERT: O 5 PHE cc_start: 0.7968 (m-80) cc_final: 0.7587 (m-80) REVERT: O 36 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6608 (tptp) REVERT: O 69 GLU cc_start: 0.7884 (tp30) cc_final: 0.7484 (tp30) REVERT: O 70 ILE cc_start: 0.8348 (tp) cc_final: 0.7715 (pt) REVERT: I 111 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8773 (ttmm) REVERT: I 184 ASP cc_start: 0.8142 (m-30) cc_final: 0.7754 (m-30) REVERT: K 306 ARG cc_start: 0.8135 (mmt90) cc_final: 0.7839 (mmp-170) REVERT: L 61 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8215 (mp) REVERT: L 62 ASN cc_start: 0.8546 (m-40) cc_final: 0.8257 (m110) REVERT: L 213 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: M 26 SER cc_start: 0.8432 (m) cc_final: 0.8012 (p) REVERT: M 72 ASP cc_start: 0.8474 (m-30) cc_final: 0.8113 (m-30) REVERT: M 91 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7362 (tm-30) REVERT: M 187 ASP cc_start: 0.7969 (m-30) cc_final: 0.7756 (m-30) REVERT: M 247 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.8158 (tpp-160) REVERT: M 251 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8578 (mtt) REVERT: N 74 ILE cc_start: 0.8507 (mt) cc_final: 0.8303 (mm) REVERT: N 84 MET cc_start: 0.5765 (mmm) cc_final: 0.5045 (tpt) REVERT: N 163 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8435 (mt-10) REVERT: N 176 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7769 (tp30) outliers start: 48 outliers final: 27 residues processed: 241 average time/residue: 0.7237 time to fit residues: 189.6061 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 : 0.452 ------------------------------------------------------------------------------- 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 111 LYS Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain 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 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 M residue 330 ASN Chi-restraints excluded: chain M residue 336 ASP 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 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: 7.9990 chunk 43 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.117481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.089992 restraints weight = 24767.373| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.89 r_work: 0.3138 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16910 Z= 0.142 Angle : 0.508 8.704 22967 Z= 0.281 Chirality : 0.041 0.143 2599 Planarity : 0.004 0.045 2825 Dihedral : 13.256 89.387 2827 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.99 % Allowed : 23.20 % Favored : 73.81 % 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: 0.83 (0.19), residues: 1995 helix: 1.46 (0.18), residues: 840 sheet: 0.57 (0.27), residues: 385 loop : -0.40 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 27 TYR 0.013 0.001 TYR L 315 PHE 0.014 0.001 PHE F 20 TRP 0.002 0.001 TRP O 20 HIS 0.003 0.000 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (16910) covalent geometry : angle 0.50849 / 0.28 (22967) hydrogen bonds : bond 0.04065 / 3.36 ( 827) hydrogen bonds : angle 4.47244 / 4.99 ( 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 253 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.576 Fit side-chains REVERT: O 5 PHE cc_start: 0.7923 (m-80) cc_final: 0.7529 (m-80) REVERT: O 21 GLU cc_start: 0.7641 (mp0) cc_final: 0.7003 (pm20) REVERT: O 70 ILE cc_start: 0.8350 (tp) cc_final: 0.7708 (pt) REVERT: I 26 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7419 (p) REVERT: I 111 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8774 (ttmm) REVERT: I 184 ASP cc_start: 0.8121 (m-30) cc_final: 0.7738 (m-30) REVERT: I 326 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8803 (ttm) REVERT: J 27 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7546 (mmm-85) REVERT: K 306 ARG cc_start: 0.8115 (mmt90) cc_final: 0.7828 (mmp-170) REVERT: L 61 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8146 (mp) REVERT: L 62 ASN cc_start: 0.8509 (m-40) cc_final: 0.8266 (m110) REVERT: L 70 LYS cc_start: 0.8326 (mmtp) cc_final: 0.8107 (mmtm) REVERT: L 213 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: M 26 SER cc_start: 0.8440 (m) cc_final: 0.7992 (p) REVERT: M 72 ASP cc_start: 0.8462 (m-30) cc_final: 0.8078 (m-30) REVERT: M 91 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7327 (tm-30) REVERT: M 187 ASP cc_start: 0.7958 (m-30) cc_final: 0.7714 (m-30) REVERT: M 205 TYR cc_start: 0.8833 (m-10) cc_final: 0.8621 (m-80) REVERT: N 74 ILE cc_start: 0.8501 (mt) cc_final: 0.8295 (mm) REVERT: N 84 MET cc_start: 0.5740 (mmm) cc_final: 0.5061 (tpt) REVERT: N 176 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7728 (tp30) outliers start: 49 outliers final: 23 residues processed: 239 average time/residue: 0.7420 time to fit residues: 193.1975 Evaluate side-chains 222 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 111 LYS Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain L residue 26 SER 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 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 38 VAL Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 202 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 183 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 101 optimal weight: 0.0980 chunk 187 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.116337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.088764 restraints weight = 24778.434| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.89 r_work: 0.3119 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16910 Z= 0.175 Angle : 0.537 8.927 22967 Z= 0.296 Chirality : 0.043 0.157 2599 Planarity : 0.004 0.044 2825 Dihedral : 13.279 89.099 2827 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.11 % Allowed : 23.32 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 1995 helix: 1.37 (0.18), residues: 846 sheet: 0.51 (0.27), residues: 385 loop : -0.39 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 2 TYR 0.015 0.001 TYR L 315 PHE 0.014 0.002 PHE F 20 TRP 0.002 0.001 TRP O 9 HIS 0.004 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (16910) covalent geometry : angle 0.53729 / 0.30 (22967) hydrogen bonds : bond 0.04513 / 3.75 ( 827) hydrogen bonds : angle 4.54989 / 5.06 ( 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 254 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.559 Fit side-chains REVERT: O 5 PHE cc_start: 0.7932 (m-80) cc_final: 0.7558 (m-80) REVERT: O 21 GLU cc_start: 0.7719 (mp0) cc_final: 0.7041 (pm20) REVERT: O 70 ILE cc_start: 0.8396 (tp) cc_final: 0.7829 (pt) REVERT: I 26 SER cc_start: 0.7950 (OUTLIER) cc_final: 0.7442 (p) REVERT: I 184 ASP cc_start: 0.8116 (m-30) cc_final: 0.7732 (m-30) REVERT: I 306 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6920 (ptm-80) REVERT: I 326 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8793 (ttm) REVERT: J 27 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7563 (mmm-85) REVERT: K 306 ARG cc_start: 0.8138 (mmt90) cc_final: 0.7862 (mmp-170) REVERT: L 61 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8140 (mp) REVERT: L 62 ASN cc_start: 0.8499 (m-40) cc_final: 0.8272 (m110) REVERT: L 70 LYS cc_start: 0.8331 (mmtp) cc_final: 0.8114 (mmtm) REVERT: L 213 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: M 26 SER cc_start: 0.8367 (m) cc_final: 0.7942 (p) REVERT: M 72 ASP cc_start: 0.8464 (m-30) cc_final: 0.8069 (m-30) REVERT: M 91 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7348 (tm-30) REVERT: M 187 ASP cc_start: 0.8008 (m-30) cc_final: 0.7724 (m-30) REVERT: M 247 ARG cc_start: 0.8525 (mtp-110) cc_final: 0.8279 (tpp-160) REVERT: N 84 MET cc_start: 0.5819 (mmm) cc_final: 0.4991 (tpt) REVERT: N 163 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: N 176 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7711 (tp30) outliers start: 51 outliers final: 26 residues processed: 243 average time/residue: 0.7464 time to fit residues: 197.6160 Evaluate side-chains 231 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 306 ARG Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain L residue 26 SER 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 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 87 THR Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 121 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 139 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 182 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 156 optimal weight: 0.0000 chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.119513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.091492 restraints weight = 24582.403| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.92 r_work: 0.3167 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16910 Z= 0.106 Angle : 0.478 8.798 22967 Z= 0.265 Chirality : 0.040 0.140 2599 Planarity : 0.003 0.046 2825 Dihedral : 13.290 87.596 2827 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.08 % Allowed : 24.24 % Favored : 73.69 % 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: 0.95 (0.19), residues: 1995 helix: 1.55 (0.18), residues: 846 sheet: 0.59 (0.27), residues: 385 loop : -0.31 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 2 TYR 0.008 0.001 TYR M 315 PHE 0.012 0.001 PHE F 20 TRP 0.004 0.000 TRP O 9 HIS 0.001 0.000 HIS J 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.11 (16910) covalent geometry : angle 0.47802 / 0.27 (22967) hydrogen bonds : bond 0.03286 / 2.71 ( 827) hydrogen bonds : angle 4.20116 / 4.71 ( 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 240 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.664 Fit side-chains REVERT: O 5 PHE cc_start: 0.7907 (m-80) cc_final: 0.7603 (m-80) REVERT: O 21 GLU cc_start: 0.7686 (mp0) cc_final: 0.7108 (pm20) REVERT: O 70 ILE cc_start: 0.8383 (tp) cc_final: 0.7828 (pt) REVERT: I 26 SER cc_start: 0.7888 (OUTLIER) cc_final: 0.7385 (p) REVERT: I 184 ASP cc_start: 0.8098 (m-30) cc_final: 0.7710 (m-30) REVERT: I 326 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8796 (ttm) REVERT: J 27 ARG cc_start: 0.8008 (mmm160) cc_final: 0.7541 (mmm-85) REVERT: J 64 LYS cc_start: 0.7957 (tttm) cc_final: 0.7730 (ttmm) REVERT: K 306 ARG cc_start: 0.8136 (mmt90) cc_final: 0.7858 (mmp-170) REVERT: L 61 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8153 (mp) REVERT: L 62 ASN cc_start: 0.8440 (m-40) cc_final: 0.8174 (m110) REVERT: L 184 ASP cc_start: 0.7846 (t0) cc_final: 0.7641 (t0) REVERT: M 26 SER cc_start: 0.8289 (m) cc_final: 0.7828 (p) REVERT: M 27 ARG cc_start: 0.7407 (tpp-160) cc_final: 0.6926 (mtt90) REVERT: M 72 ASP cc_start: 0.8475 (m-30) cc_final: 0.8108 (m-30) REVERT: M 91 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7344 (tm-30) REVERT: M 187 ASP cc_start: 0.7986 (m-30) cc_final: 0.7674 (m-30) REVERT: M 206 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7561 (mp-120) REVERT: M 247 ARG cc_start: 0.8520 (mtp-110) cc_final: 0.8236 (tpp-160) REVERT: N 84 MET cc_start: 0.5760 (mmm) cc_final: 0.5057 (tpt) REVERT: N 163 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8437 (mt-10) REVERT: N 176 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7718 (tp30) REVERT: N 202 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7622 (mp-120) outliers start: 34 outliers final: 15 residues processed: 231 average time/residue: 0.7403 time to fit residues: 186.1100 Evaluate side-chains 216 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 ARG 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 326 MET Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 251 MET Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 206 GLN Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 121 SER 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: 0.9980 chunk 126 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 112 optimal weight: 0.0030 overall best weight: 1.9994 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.117772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089269 restraints weight = 24638.669| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.93 r_work: 0.3124 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2140 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= 0.154 Angle : 0.516 8.598 22967 Z= 0.284 Chirality : 0.042 0.152 2599 Planarity : 0.004 0.049 2825 Dihedral : 13.195 88.858 2826 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.14 % Allowed : 24.18 % Favored : 73.69 % 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: 0.94 (0.19), residues: 1995 helix: 1.60 (0.18), residues: 840 sheet: 0.54 (0.27), residues: 385 loop : -0.35 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 2 TYR 0.013 0.001 TYR L 315 PHE 0.013 0.001 PHE F 20 TRP 0.004 0.001 TRP O 9 HIS 0.004 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (16910) covalent geometry : angle 0.51596 / 0.28 (22967) hydrogen bonds : bond 0.04020 / 3.34 ( 827) hydrogen bonds : angle 4.35205 / 4.88 ( 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 233 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.681 Fit side-chains REVERT: O 5 PHE cc_start: 0.7930 (m-80) cc_final: 0.7558 (m-80) REVERT: O 21 GLU cc_start: 0.7740 (mp0) cc_final: 0.7109 (pm20) REVERT: O 70 ILE cc_start: 0.8373 (tp) cc_final: 0.7832 (pt) REVERT: I 184 ASP cc_start: 0.8160 (m-30) cc_final: 0.7780 (m-30) REVERT: I 326 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8801 (ttm) REVERT: J 27 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7557 (mmm-85) REVERT: J 64 LYS cc_start: 0.8015 (tttm) cc_final: 0.7793 (ttmm) REVERT: K 306 ARG cc_start: 0.8135 (mmt90) cc_final: 0.7829 (mmp-170) REVERT: L 61 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8161 (mp) REVERT: L 62 ASN cc_start: 0.8412 (m-40) cc_final: 0.8161 (m110) REVERT: L 213 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: M 26 SER cc_start: 0.8309 (m) cc_final: 0.7848 (p) REVERT: M 72 ASP cc_start: 0.8481 (m-30) cc_final: 0.8084 (m-30) REVERT: M 91 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7340 (tm-30) REVERT: N 84 MET cc_start: 0.5769 (mmm) cc_final: 0.4966 (tpt) REVERT: N 163 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8470 (mt-10) REVERT: N 176 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7722 (tp30) outliers start: 35 outliers final: 17 residues processed: 224 average time/residue: 0.8175 time to fit residues: 199.0798 Evaluate side-chains 216 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 326 MET Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain L residue 230 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 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 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: 6.9990 chunk 146 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.117154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088622 restraints weight = 24629.460| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.94 r_work: 0.3117 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16910 Z= 0.168 Angle : 0.536 8.741 22967 Z= 0.293 Chirality : 0.043 0.200 2599 Planarity : 0.004 0.045 2825 Dihedral : 13.277 89.928 2826 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.26 % Allowed : 24.18 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.19), residues: 1995 helix: 1.53 (0.18), residues: 840 sheet: 0.50 (0.27), residues: 385 loop : -0.37 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 27 TYR 0.013 0.001 TYR L 315 PHE 0.013 0.001 PHE F 20 TRP 0.003 0.001 TRP O 9 HIS 0.004 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (16910) covalent geometry : angle 0.53627 / 0.29 (22967) hydrogen bonds : bond 0.04260 / 3.53 ( 827) hydrogen bonds : angle 4.44307 / 4.98 ( 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 234 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.599 Fit side-chains REVERT: O 5 PHE cc_start: 0.7886 (m-80) cc_final: 0.7545 (m-80) REVERT: O 21 GLU cc_start: 0.7688 (mp0) cc_final: 0.7127 (pm20) REVERT: O 70 ILE cc_start: 0.8393 (tp) cc_final: 0.7855 (pt) REVERT: I 26 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7490 (p) REVERT: I 326 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8790 (ttm) REVERT: J 27 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7549 (mmm-85) REVERT: J 43 GLU cc_start: 0.7970 (pp20) cc_final: 0.7611 (pp20) REVERT: J 64 LYS cc_start: 0.8012 (tttm) cc_final: 0.7790 (ttmm) REVERT: K 306 ARG cc_start: 0.8129 (mmt90) cc_final: 0.7803 (mmp-170) REVERT: L 61 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8192 (mp) REVERT: L 62 ASN cc_start: 0.8425 (m-40) cc_final: 0.8152 (m110) REVERT: L 213 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: M 26 SER cc_start: 0.8346 (m) cc_final: 0.7903 (p) REVERT: M 72 ASP cc_start: 0.8479 (m-30) cc_final: 0.8087 (m-30) REVERT: M 91 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7338 (tm-30) REVERT: M 247 ARG cc_start: 0.8512 (mtp-110) cc_final: 0.8235 (tpp-160) REVERT: N 84 MET cc_start: 0.5883 (mmm) cc_final: 0.5021 (tpt) REVERT: N 163 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8473 (mt-10) REVERT: N 176 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7716 (tp30) outliers start: 37 outliers final: 20 residues processed: 226 average time/residue: 0.7362 time to fit residues: 181.2878 Evaluate side-chains 219 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 ARG 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 326 MET Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 66 ILE 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 183 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain L residue 230 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 N residue 38 VAL Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 121 SER 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: 2.9990 chunk 153 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.117478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.089032 restraints weight = 24539.571| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.10 r_work: 0.3109 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2245 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= 0.155 Angle : 0.533 8.778 22967 Z= 0.292 Chirality : 0.043 0.303 2599 Planarity : 0.004 0.056 2825 Dihedral : 13.307 89.907 2825 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.95 % Allowed : 24.48 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 1995 helix: 1.53 (0.18), residues: 840 sheet: 0.51 (0.27), residues: 385 loop : -0.36 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 27 TYR 0.012 0.001 TYR L 315 PHE 0.013 0.001 PHE F 20 TRP 0.004 0.001 TRP O 9 HIS 0.003 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (16910) covalent geometry : angle 0.53323 / 0.29 (22967) hydrogen bonds : bond 0.04114 / 3.42 ( 827) hydrogen bonds : angle 4.42586 / 4.98 ( 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 230 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.672 Fit side-chains REVERT: O 5 PHE cc_start: 0.7855 (m-80) cc_final: 0.7495 (m-80) REVERT: O 21 GLU cc_start: 0.7684 (mp0) cc_final: 0.7145 (pm20) REVERT: O 70 ILE cc_start: 0.8350 (tp) cc_final: 0.7787 (pp) REVERT: I 26 SER cc_start: 0.7928 (OUTLIER) cc_final: 0.7441 (p) REVERT: I 184 ASP cc_start: 0.8217 (m-30) cc_final: 0.7820 (m-30) REVERT: I 326 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8809 (ttm) REVERT: J 27 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7552 (mmm-85) REVERT: J 43 GLU cc_start: 0.7996 (pp20) cc_final: 0.7694 (pp20) REVERT: J 64 LYS cc_start: 0.8038 (tttm) cc_final: 0.7816 (ttmm) REVERT: K 306 ARG cc_start: 0.8176 (mmt90) cc_final: 0.7824 (mmp-170) REVERT: L 61 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8225 (mp) REVERT: L 62 ASN cc_start: 0.8452 (m-40) cc_final: 0.8181 (m110) REVERT: L 213 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: M 26 SER cc_start: 0.8364 (m) cc_final: 0.7887 (p) REVERT: M 27 ARG cc_start: 0.7439 (tpp-160) cc_final: 0.6914 (mpt90) REVERT: M 72 ASP cc_start: 0.8484 (m-30) cc_final: 0.8092 (m-30) REVERT: M 91 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7232 (tm-30) REVERT: M 247 ARG cc_start: 0.8515 (mtp-110) cc_final: 0.8249 (tpp-160) REVERT: N 84 MET cc_start: 0.5882 (mmm) cc_final: 0.5029 (tpt) REVERT: N 163 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8480 (mt-10) REVERT: N 176 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7778 (tp30) outliers start: 32 outliers final: 21 residues processed: 222 average time/residue: 0.8335 time to fit residues: 201.2010 Evaluate side-chains 223 residues out of total 1647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 ARG 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 326 MET Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 66 ILE 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 183 SER Chi-restraints excluded: chain L residue 213 GLU Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 181 SER Chi-restraints excluded: chain M residue 202 GLN Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 99 ILE Chi-restraints excluded: chain N residue 121 SER 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: 0.8980 chunk 164 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN I 30 GLN J 30 GLN J 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.116921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.088562 restraints weight = 24638.350| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.10 r_work: 0.3102 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16910 Z= 0.174 Angle : 0.552 8.661 22967 Z= 0.301 Chirality : 0.043 0.250 2599 Planarity : 0.004 0.048 2825 Dihedral : 13.339 89.241 2825 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.89 % Allowed : 24.79 % 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: 0.82 (0.19), residues: 1995 helix: 1.49 (0.18), residues: 840 sheet: 0.48 (0.27), residues: 385 loop : -0.40 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 27 TYR 0.013 0.001 TYR L 315 PHE 0.013 0.001 PHE F 20 TRP 0.003 0.001 TRP O 9 HIS 0.004 0.001 HIS K 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (16910) covalent geometry : angle 0.55241 / 0.30 (22967) hydrogen bonds : bond 0.04390 / 3.65 ( 827) hydrogen bonds : angle 4.50987 / 5.06 ( 2262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7346.11 seconds wall clock time: 125 minutes 22.54 seconds (7522.54 seconds total)