Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 03:50:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/08_2023/6put_20481.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/08_2023/6put_20481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/08_2023/6put_20481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/08_2023/6put_20481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/08_2023/6put_20481.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/08_2023/6put_20481.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.029 sd= 0.707 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 66 5.49 5 S 32 5.16 5 C 6610 2.51 5 N 1886 2.21 5 O 2374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 11": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C ASP 232": "OD1" <-> "OD2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D ASP 253": "OD1" <-> "OD2" Residue "G PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 11": "OE1" <-> "OE2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 25": "OD1" <-> "OD2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H ASP 116": "OD1" <-> "OD2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H ASP 167": "OD1" <-> "OD2" Residue "H ASP 202": "OD1" <-> "OD2" Residue "H TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 256": "OD1" <-> "OD2" Residue "I ASP 229": "OD1" <-> "OD2" Residue "I ASP 232": "OD1" <-> "OD2" Residue "I GLU 246": "OE1" <-> "OE2" Residue "I ASP 270": "OD1" <-> "OD2" Residue "J ASP 229": "OD1" <-> "OD2" Residue "J ASP 253": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 10976 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1905 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Chain: "B" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1818 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 4 Chain: "C" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 526 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "F" Number of atoms: 331 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 362 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1905 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Chain: "H" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1818 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 7, 'TRANS': 223} Chain breaks: 4 Chain: "I" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 526 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "J" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "K" Number of atoms: 331 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "L" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 362 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 317 SG CYS A 40 25.667 45.428 50.550 1.00 37.03 S ATOM 340 SG CYS A 43 29.185 46.359 49.087 1.00 16.24 S ATOM 2224 SG CYS B 40 49.443 121.657 21.753 1.00103.27 S ATOM 5805 SG CYS G 40 64.393 87.292 50.550 1.00 37.03 S ATOM 5828 SG CYS G 43 60.875 86.361 49.087 1.00 16.24 S ATOM 7712 SG CYS H 40 40.617 11.063 21.753 1.00103.27 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.50 ... (19 atoms not shown) pdb=" C4 A DA F 21 " occ=0.50 residue: pdb=" P A DA K 21 " occ=0.50 ... (19 atoms not shown) pdb=" C4 A DA K 21 " occ=0.50 Time building chain proxies: 6.14, per 1000 atoms: 0.56 Number of scatterers: 10976 At special positions: 0 Unit cell: (90.85, 133.51, 82.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 32 16.00 P 66 15.00 O 2374 8.00 N 1886 7.00 C 6610 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 40 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 16 " pdb=" ZN G 303 " pdb="ZN ZN G 303 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 303 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 43 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 40 " pdb=" ZN H 500 " pdb="ZN ZN H 500 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 40 " pdb="ZN ZN H 500 " - pdb=" ND1 HIS H 16 " Number of angles added : 2 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 14 sheets defined 47.0% alpha, 18.5% beta 28 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 WARNING: missing atoms! removed outlier: 4.017A pdb=" N LYS A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.678A pdb=" N CYS A 43 " --> pdb=" O CYS A 40 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 44 " --> pdb=" O ASP A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 44' Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 165 Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.507A pdb=" N ALA A 169 " --> pdb=" O ARG A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 195 through 219 removed outlier: 3.629A pdb=" N VAL A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 16 Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.520A pdb=" N PHE B 26 " --> pdb=" O MET B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.701A pdb=" N CYS B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 151 through 166 Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 172 through 186 removed outlier: 3.828A pdb=" N GLN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET B 178 " --> pdb=" O THR B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 221 removed outlier: 3.627A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'G' and resid 3 through 16 WARNING: missing atoms! removed outlier: 4.017A pdb=" N LYS G 14 " --> pdb=" O GLU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 26 Processing helix chain 'G' and resid 29 through 39 Processing helix chain 'G' and resid 40 through 44 removed outlier: 3.678A pdb=" N CYS G 43 " --> pdb=" O CYS G 40 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN G 44 " --> pdb=" O ASP G 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 44' Processing helix chain 'G' and resid 93 through 108 Processing helix chain 'G' and resid 118 through 123 Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 144 through 147 Processing helix chain 'G' and resid 148 through 165 Processing helix chain 'G' and resid 166 through 169 removed outlier: 3.507A pdb=" N ALA G 169 " --> pdb=" O ARG G 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 166 through 169' Processing helix chain 'G' and resid 171 through 186 Processing helix chain 'G' and resid 195 through 219 removed outlier: 3.629A pdb=" N VAL G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS G 219 " --> pdb=" O LYS G 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 16 Processing helix chain 'H' and resid 18 through 26 removed outlier: 3.520A pdb=" N PHE H 26 " --> pdb=" O MET H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.701A pdb=" N CYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 108 Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 151 through 166 Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 172 through 186 removed outlier: 3.828A pdb=" N GLN H 177 " --> pdb=" O LYS H 173 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET H 178 " --> pdb=" O THR H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 221 removed outlier: 3.627A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 222 Processing sheet with id= 1, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.069A pdb=" N VAL A 113 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 64 through 68 Processing sheet with id= 3, first strand: chain 'A' and resid 241 through 244 Processing sheet with id= 4, first strand: chain 'B' and resid 84 through 89 removed outlier: 4.319A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.207A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 256 through 261 removed outlier: 6.463A pdb=" N GLN C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU C 241 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLY C 237 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR C 227 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 257 through 261 removed outlier: 6.578A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL D 225 " --> pdb=" O PRO D 238 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'G' and resid 60 through 61 removed outlier: 6.069A pdb=" N VAL G 113 " --> pdb=" O GLU G 138 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'G' and resid 64 through 68 Processing sheet with id= 10, first strand: chain 'G' and resid 241 through 244 Processing sheet with id= 11, first strand: chain 'H' and resid 84 through 89 removed outlier: 4.319A pdb=" N VAL H 72 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 240 through 244 removed outlier: 6.207A pdb=" N LEU H 241 " --> pdb=" O GLN H 252 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN H 252 " --> pdb=" O LEU H 241 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 256 through 261 removed outlier: 6.463A pdb=" N GLN I 252 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU I 241 " --> pdb=" O GLN I 252 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLY I 237 " --> pdb=" O TYR I 227 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR I 227 " --> pdb=" O GLY I 237 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'J' and resid 257 through 261 removed outlier: 6.578A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL J 225 " --> pdb=" O PRO J 238 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2336 1.33 - 1.45: 2572 1.45 - 1.57: 5926 1.57 - 1.69: 130 1.69 - 1.81: 46 Bond restraints: 11010 Sorted by residual: bond pdb=" C LYS A 127 " pdb=" N ALA A 128 " ideal model delta sigma weight residual 1.335 1.480 -0.145 1.38e-02 5.25e+03 1.10e+02 bond pdb=" C LYS G 127 " pdb=" N ALA G 128 " ideal model delta sigma weight residual 1.335 1.480 -0.145 1.38e-02 5.25e+03 1.10e+02 bond pdb=" N THR G 122 " pdb=" CA THR G 122 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.33e-02 5.65e+03 7.39e+00 bond pdb=" N THR A 122 " pdb=" CA THR A 122 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.33e-02 5.65e+03 7.39e+00 bond pdb=" C ASP G 116 " pdb=" N ASN G 117 " ideal model delta sigma weight residual 1.334 1.302 0.032 1.24e-02 6.50e+03 6.59e+00 ... (remaining 11005 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.65: 706 106.65 - 113.49: 6070 113.49 - 120.34: 4118 120.34 - 127.18: 3980 127.18 - 134.03: 264 Bond angle restraints: 15138 Sorted by residual: angle pdb=" O LYS A 127 " pdb=" C LYS A 127 " pdb=" N ALA A 128 " ideal model delta sigma weight residual 122.15 109.65 12.50 1.14e+00 7.69e-01 1.20e+02 angle pdb=" O LYS G 127 " pdb=" C LYS G 127 " pdb=" N ALA G 128 " ideal model delta sigma weight residual 122.15 109.65 12.50 1.14e+00 7.69e-01 1.20e+02 angle pdb=" CA LYS G 127 " pdb=" C LYS G 127 " pdb=" N ALA G 128 " ideal model delta sigma weight residual 117.39 129.82 -12.43 1.24e+00 6.50e-01 1.01e+02 angle pdb=" CA LYS A 127 " pdb=" C LYS A 127 " pdb=" N ALA A 128 " ideal model delta sigma weight residual 117.39 129.82 -12.43 1.24e+00 6.50e-01 1.01e+02 angle pdb=" O ASP G 116 " pdb=" C ASP G 116 " pdb=" N ASN G 117 " ideal model delta sigma weight residual 121.83 133.32 -11.49 1.28e+00 6.10e-01 8.05e+01 ... (remaining 15133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5392 17.65 - 35.30: 556 35.30 - 52.95: 300 52.95 - 70.61: 76 70.61 - 88.26: 16 Dihedral angle restraints: 6340 sinusoidal: 2990 harmonic: 3350 Sorted by residual: dihedral pdb=" CA TYR A 194 " pdb=" C TYR A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA TYR G 194 " pdb=" C TYR G 194 " pdb=" N SER G 195 " pdb=" CA SER G 195 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA TYR C 271 " pdb=" C TYR C 271 " pdb=" N GLY C 272 " pdb=" CA GLY C 272 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 6337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1260 0.055 - 0.110: 344 0.110 - 0.164: 70 0.164 - 0.219: 8 0.219 - 0.274: 2 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CB VAL B 165 " pdb=" CA VAL B 165 " pdb=" CG1 VAL B 165 " pdb=" CG2 VAL B 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL H 165 " pdb=" CA VAL H 165 " pdb=" CG1 VAL H 165 " pdb=" CG2 VAL H 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ASN B 117 " pdb=" N ASN B 117 " pdb=" C ASN B 117 " pdb=" CB ASN B 117 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1681 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 57 " -0.041 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO B 58 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 57 " 0.041 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO H 58 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 58 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 58 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 116 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C ASP H 116 " -0.038 2.00e-02 2.50e+03 pdb=" O ASP H 116 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN H 117 " 0.012 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 10 0.98 - 1.96: 2 1.96 - 2.94: 4320 2.94 - 3.92: 29776 3.92 - 4.90: 59558 Warning: very small nonbonded interaction distances. Nonbonded interactions: 93666 Sorted by model distance: nonbonded pdb=" O HOH A 438 " pdb=" O HOH K 110 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 459 " pdb=" O HOH G 469 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 469 " pdb=" O HOH G 459 " model vdw 0.000 2.440 nonbonded pdb=" O HOH F 110 " pdb=" O HOH G 438 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 477 " pdb=" O HOH G 478 " model vdw 0.001 2.440 ... (remaining 93661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 44 or resid 57 through 139 or resid 150 through \ 261 or resid 303)) selection = (chain 'B' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name CB or name CG1 or name CG2 or name CD1)) or resid 6 through 16 or (resid \ 17 and (name N or name CA or name C or name CB or name OG )) or resid 18 through \ 61 or (resid 62 and (name N or name CA or name C or name CB or name CG or name \ CD or name OE1 or name NE2)) or resid 63 through 86 or (resid 87 and (name N or \ name CA or name C or name CB or name CG or name CD or name OE1 or name OE2)) or \ resid 88 through 226 or resid 240 through 252 or resid 257 through 261 or resid \ 500)) selection = (chain 'G' and (resid 1 through 44 or resid 57 through 139 or resid 150 through \ 261 or resid 303)) selection = (chain 'H' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name CB or name CG1 or name CG2 or name CD1)) or resid 6 through 16 or (resid \ 17 and (name N or name CA or name C or name CB or name OG )) or resid 18 through \ 61 or (resid 62 and (name N or name CA or name C or name CB or name CG or name \ CD or name OE1 or name NE2)) or resid 63 through 86 or (resid 87 and (name N or \ name CA or name C or name CB or name CG or name CD or name OE1 or name OE2)) or \ resid 88 through 226 or resid 240 through 252 or resid 257 through 261 or resid \ 500)) } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'K' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.870 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.360 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.110 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 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 : 0.007 0.145 11010 Z= 0.419 Angle : 0.824 12.664 15138 Z= 0.519 Chirality : 0.053 0.274 1684 Planarity : 0.007 0.061 1668 Dihedral : 19.070 88.257 4172 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.19), residues: 1130 helix: -2.36 (0.16), residues: 494 sheet: -1.30 (0.31), residues: 216 loop : -2.46 (0.24), residues: 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 1.168 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 240 average time/residue: 1.2819 time to fit residues: 330.9640 Evaluate side-chains 182 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2144 time to fit residues: 2.1401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 0.0010 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS B 9 GLN B 216 GLN B 221 GLN H 12 HIS ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.144 11010 Z= 0.281 Angle : 0.914 23.219 15138 Z= 0.496 Chirality : 0.051 0.362 1684 Planarity : 0.013 0.253 1668 Dihedral : 21.672 149.984 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.71 % Allowed : 4.69 % Favored : 94.60 % Rotamer Outliers : 3.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.21), residues: 1130 helix: -1.55 (0.19), residues: 498 sheet: -1.26 (0.31), residues: 216 loop : -2.52 (0.24), residues: 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 210 time to evaluate : 1.285 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. outliers start: 37 outliers final: 4 residues processed: 229 average time/residue: 1.0342 time to fit residues: 258.9518 Evaluate side-chains 175 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1044 time to fit residues: 1.9407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 29 optimal weight: 0.0470 chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN B 252 GLN G 183 HIS H 164 GLN H 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 11010 Z= 0.188 Angle : 0.506 6.056 15138 Z= 0.289 Chirality : 0.041 0.142 1684 Planarity : 0.004 0.042 1668 Dihedral : 21.477 177.402 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.23), residues: 1130 helix: 0.08 (0.22), residues: 500 sheet: -0.52 (0.33), residues: 226 loop : -2.18 (0.26), residues: 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 1.250 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. outliers start: 19 outliers final: 10 residues processed: 194 average time/residue: 1.0229 time to fit residues: 217.4968 Evaluate side-chains 178 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 3 residues processed: 7 average time/residue: 0.1058 time to fit residues: 2.8973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN G 67 HIS G 148 GLN G 216 GLN H 221 GLN ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 11010 Z= 0.258 Angle : 0.505 5.590 15138 Z= 0.287 Chirality : 0.043 0.132 1684 Planarity : 0.004 0.043 1668 Dihedral : 21.519 176.246 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1130 helix: 0.93 (0.22), residues: 498 sheet: -0.39 (0.33), residues: 216 loop : -1.84 (0.28), residues: 416 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 1.152 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. outliers start: 27 outliers final: 15 residues processed: 187 average time/residue: 1.0483 time to fit residues: 215.3151 Evaluate side-chains 186 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 8 average time/residue: 0.1025 time to fit residues: 2.9625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN G 216 GLN H 221 GLN ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 11010 Z= 0.307 Angle : 0.521 5.702 15138 Z= 0.296 Chirality : 0.044 0.134 1684 Planarity : 0.004 0.043 1668 Dihedral : 21.558 176.248 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1130 helix: 1.18 (0.22), residues: 498 sheet: -0.22 (0.33), residues: 216 loop : -1.61 (0.29), residues: 416 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.164 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. outliers start: 22 outliers final: 13 residues processed: 189 average time/residue: 1.0467 time to fit residues: 216.7601 Evaluate side-chains 182 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.1162 time to fit residues: 2.8390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 0.3980 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 221 GLN G 216 GLN H 221 GLN ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 11010 Z= 0.204 Angle : 0.494 5.700 15138 Z= 0.281 Chirality : 0.042 0.150 1684 Planarity : 0.003 0.043 1668 Dihedral : 21.514 177.505 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1130 helix: 1.45 (0.22), residues: 498 sheet: -0.11 (0.33), residues: 216 loop : -1.42 (0.30), residues: 416 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 1.266 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. outliers start: 18 outliers final: 10 residues processed: 184 average time/residue: 1.0729 time to fit residues: 216.0306 Evaluate side-chains 177 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.1271 time to fit residues: 2.2065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN G 114 HIS G 148 GLN H 221 GLN H 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11010 Z= 0.209 Angle : 0.487 5.675 15138 Z= 0.277 Chirality : 0.042 0.132 1684 Planarity : 0.003 0.042 1668 Dihedral : 21.416 177.611 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1130 helix: 1.61 (0.23), residues: 496 sheet: 0.20 (0.33), residues: 226 loop : -1.27 (0.31), residues: 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 1.208 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. outliers start: 17 outliers final: 12 residues processed: 186 average time/residue: 1.0424 time to fit residues: 212.4306 Evaluate side-chains 185 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.0983 time to fit residues: 2.2685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN G 117 ASN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 11010 Z= 0.286 Angle : 0.520 5.615 15138 Z= 0.293 Chirality : 0.044 0.129 1684 Planarity : 0.004 0.041 1668 Dihedral : 21.532 176.493 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1130 helix: 1.59 (0.22), residues: 498 sheet: 0.02 (0.33), residues: 216 loop : -1.22 (0.31), residues: 416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 1.163 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. outliers start: 19 outliers final: 13 residues processed: 188 average time/residue: 1.0374 time to fit residues: 213.5520 Evaluate side-chains 184 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.0933 time to fit residues: 2.2003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.0470 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.0040 chunk 83 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN G 117 ASN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11010 Z= 0.165 Angle : 0.497 6.739 15138 Z= 0.282 Chirality : 0.042 0.136 1684 Planarity : 0.003 0.040 1668 Dihedral : 21.493 178.357 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1130 helix: 1.75 (0.23), residues: 496 sheet: 0.12 (0.33), residues: 216 loop : -1.14 (0.31), residues: 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 1.185 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. outliers start: 13 outliers final: 9 residues processed: 183 average time/residue: 1.0229 time to fit residues: 205.5143 Evaluate side-chains 179 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 170 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.6482 time to fit residues: 3.0060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN H 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11010 Z= 0.202 Angle : 0.494 6.605 15138 Z= 0.279 Chirality : 0.042 0.130 1684 Planarity : 0.003 0.042 1668 Dihedral : 21.399 177.711 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1130 helix: 1.84 (0.23), residues: 496 sheet: 0.32 (0.33), residues: 226 loop : -1.11 (0.31), residues: 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.064 Fit side-chains TARDY: cannot create tardy model for: "ILE A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU A 87 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 87 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 8 residues processed: 180 average time/residue: 0.9517 time to fit residues: 188.7126 Evaluate side-chains 178 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.1521 time to fit residues: 1.7283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 221 GLN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.098952 restraints weight = 11904.560| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.66 r_work: 0.2924 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 11010 Z= 0.342 Angle : 0.544 6.587 15138 Z= 0.305 Chirality : 0.045 0.135 1684 Planarity : 0.004 0.042 1668 Dihedral : 21.571 176.223 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1130 helix: 1.68 (0.22), residues: 498 sheet: 0.25 (0.33), residues: 226 loop : -1.17 (0.31), residues: 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4083.67 seconds wall clock time: 73 minutes 15.24 seconds (4395.24 seconds total)