Starting phenix.real_space_refine on Sat Dec 9 11:51:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/12_2023/6put_20481.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/12_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_20481/12_2023/6put_20481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/12_2023/6put_20481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/12_2023/6put_20481.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/12_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6.43, per 1000 atoms: 0.59 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: 4.81 Conformation dependent library (CDL) restraints added in 1.7 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: 4.29 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: 3.54 Time building geometry restraints manager: 5.15 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: 5436 17.65 - 35.30: 588 35.30 - 52.95: 300 52.95 - 70.61: 76 70.61 - 88.26: 16 Dihedral angle restraints: 6416 sinusoidal: 3066 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 6413 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: 3.420 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: 12.930 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.890 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.550 ------------------------------------------------------------------------------- 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 : 19.073 88.257 4248 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 % Allowed : 5.47 % Favored : 94.33 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 19 HIS 0.005 0.002 HIS B 12 PHE 0.015 0.002 PHE G 185 TYR 0.017 0.002 TYR B 83 ARG 0.004 0.000 ARG I 262 *********************** 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 : 1.317 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: 1.3105 time to fit residues: 337.8771 Evaluate side-chains 182 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1970 time to fit residues: 2.1361 ------------------------------------------------------------------------------- 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: 0.8693 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 11010 Z= 0.264 Angle : 0.894 22.331 15138 Z= 0.482 Chirality : 0.050 0.346 1684 Planarity : 0.012 0.227 1668 Dihedral : 21.512 153.153 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.88 % Allowed : 4.78 % Favored : 94.34 % Rotamer: Outliers : 3.85 % Allowed : 13.87 % Favored : 82.29 % 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: -2.89 (0.21), residues: 1130 helix: -1.55 (0.20), residues: 488 sheet: -1.28 (0.32), residues: 216 loop : -2.52 (0.24), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.136 0.007 TRP H 61 HIS 0.048 0.005 HIS G 171 PHE 0.104 0.005 PHE H 26 TYR 0.280 0.009 TYR G 226 ARG 0.085 0.003 ARG J 228 *********************** 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 256 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 218 time to evaluate : 1.255 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: 38 outliers final: 5 residues processed: 236 average time/residue: 1.1155 time to fit residues: 285.7853 Evaluate side-chains 176 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.1027 time to fit residues: 2.2505 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 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 ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 HIS H 164 GLN H 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11010 Z= 0.222 Angle : 0.519 6.208 15138 Z= 0.296 Chirality : 0.042 0.138 1684 Planarity : 0.004 0.042 1668 Dihedral : 21.372 177.123 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.43 % Allowed : 16.30 % Favored : 81.28 % 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: -1.40 (0.23), residues: 1130 helix: 0.01 (0.21), residues: 500 sheet: -0.78 (0.32), residues: 216 loop : -2.09 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 19 HIS 0.007 0.001 HIS H 171 PHE 0.009 0.001 PHE A 185 TYR 0.013 0.001 TYR G 194 ARG 0.004 0.000 ARG H 224 *********************** 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 207 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 1.242 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: 24 outliers final: 12 residues processed: 196 average time/residue: 1.0303 time to fit residues: 221.3849 Evaluate side-chains 181 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 8 average time/residue: 0.0991 time to fit residues: 3.0554 ------------------------------------------------------------------------------- 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: 0.9980 chunk 80 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 67 HIS G 148 GLN G 216 GLN H 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11010 Z= 0.181 Angle : 0.482 5.789 15138 Z= 0.274 Chirality : 0.041 0.131 1684 Planarity : 0.004 0.037 1668 Dihedral : 21.225 177.319 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.02 % Allowed : 18.02 % Favored : 79.96 % 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: -0.38 (0.24), residues: 1130 helix: 1.01 (0.22), residues: 498 sheet: -0.32 (0.33), residues: 216 loop : -1.76 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 19 HIS 0.006 0.001 HIS H 12 PHE 0.007 0.001 PHE H 26 TYR 0.011 0.001 TYR H 83 ARG 0.006 0.000 ARG C 262 *********************** 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 198 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 1.103 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: 20 outliers final: 9 residues processed: 190 average time/residue: 1.0505 time to fit residues: 218.0615 Evaluate side-chains 178 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.0999 time to fit residues: 2.2704 ------------------------------------------------------------------------------- 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: 0.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 0.0070 overall best weight: 0.7002 ------------------------------------------------------------------------------- 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 G 216 GLN H 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11010 Z= 0.196 Angle : 0.478 5.809 15138 Z= 0.273 Chirality : 0.041 0.134 1684 Planarity : 0.003 0.039 1668 Dihedral : 21.210 177.733 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.23 % Allowed : 18.52 % Favored : 79.25 % 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: 0.09 (0.25), residues: 1130 helix: 1.40 (0.23), residues: 496 sheet: -0.03 (0.34), residues: 216 loop : -1.53 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 243 HIS 0.005 0.001 HIS H 12 PHE 0.020 0.001 PHE H 26 TYR 0.012 0.001 TYR H 83 ARG 0.002 0.000 ARG C 262 *********************** 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 193 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.225 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: 187 average time/residue: 1.0232 time to fit residues: 209.5209 Evaluate side-chains 181 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 7 average time/residue: 0.1097 time to fit residues: 3.0479 ------------------------------------------------------------------------------- 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: 0.7980 chunk 102 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.8782 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11010 Z= 0.308 Angle : 0.523 5.597 15138 Z= 0.296 Chirality : 0.044 0.138 1684 Planarity : 0.004 0.041 1668 Dihedral : 21.437 176.350 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.23 % Allowed : 19.13 % Favored : 78.64 % 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: 0.13 (0.25), residues: 1130 helix: 1.38 (0.22), residues: 498 sheet: -0.04 (0.33), residues: 216 loop : -1.44 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 243 HIS 0.004 0.001 HIS H 12 PHE 0.011 0.001 PHE A 185 TYR 0.014 0.001 TYR A 194 ARG 0.005 0.000 ARG C 262 *********************** 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 189 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.286 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: 14 residues processed: 183 average time/residue: 1.0730 time to fit residues: 214.7329 Evaluate side-chains 181 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.1121 time to fit residues: 2.5666 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8761 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11010 Z= 0.231 Angle : 0.497 5.641 15138 Z= 0.282 Chirality : 0.042 0.133 1684 Planarity : 0.003 0.041 1668 Dihedral : 21.316 177.716 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.82 % Allowed : 20.24 % Favored : 77.94 % 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: 0.33 (0.25), residues: 1130 helix: 1.53 (0.22), residues: 496 sheet: 0.05 (0.33), residues: 216 loop : -1.29 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 243 HIS 0.005 0.001 HIS H 171 PHE 0.016 0.001 PHE B 26 TYR 0.012 0.001 TYR A 194 ARG 0.002 0.000 ARG J 228 *********************** 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: 18 poor density : 174 time to evaluate : 1.252 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: 11 residues processed: 188 average time/residue: 1.0848 time to fit residues: 223.1863 Evaluate side-chains 178 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1126 time to fit residues: 2.3858 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8770 moved from start: 0.2048 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= 0.262 Angle : 0.511 5.567 15138 Z= 0.289 Chirality : 0.043 0.132 1684 Planarity : 0.004 0.040 1668 Dihedral : 21.349 177.193 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.72 % Allowed : 20.95 % Favored : 77.33 % 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: 0.38 (0.25), residues: 1130 helix: 1.56 (0.22), residues: 496 sheet: 0.07 (0.33), residues: 216 loop : -1.23 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 243 HIS 0.006 0.001 HIS H 171 PHE 0.029 0.001 PHE H 26 TYR 0.012 0.001 TYR A 194 ARG 0.001 0.000 ARG J 228 *********************** 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 184 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 1.111 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: 181 average time/residue: 1.0565 time to fit residues: 209.0373 Evaluate side-chains 178 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.1075 time to fit residues: 2.0468 ------------------------------------------------------------------------------- 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: 0.0980 chunk 99 optimal weight: 0.5980 chunk 105 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 0.0060 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2109 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= 0.162 Angle : 0.488 6.219 15138 Z= 0.277 Chirality : 0.041 0.138 1684 Planarity : 0.003 0.039 1668 Dihedral : 21.253 178.725 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.21 % Allowed : 21.26 % Favored : 77.53 % 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: 0.59 (0.25), residues: 1130 helix: 1.76 (0.23), residues: 496 sheet: 0.19 (0.33), residues: 216 loop : -1.17 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 243 HIS 0.005 0.001 HIS H 171 PHE 0.031 0.001 PHE H 26 TYR 0.010 0.001 TYR H 83 ARG 0.002 0.000 ARG J 228 *********************** 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 183 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 1.308 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: 12 outliers final: 11 residues processed: 182 average time/residue: 1.0433 time to fit residues: 207.6501 Evaluate side-chains 176 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.0784 time to fit residues: 1.2932 ------------------------------------------------------------------------------- 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: 0.4980 chunk 53 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8746 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11010 Z= 0.208 Angle : 0.493 6.573 15138 Z= 0.279 Chirality : 0.042 0.132 1684 Planarity : 0.003 0.039 1668 Dihedral : 21.236 177.872 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.01 % Allowed : 21.66 % Favored : 77.33 % 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: 0.69 (0.25), residues: 1130 helix: 1.78 (0.22), residues: 496 sheet: 0.37 (0.33), residues: 226 loop : -1.17 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 243 HIS 0.009 0.001 HIS H 171 PHE 0.030 0.001 PHE H 26 TYR 0.011 0.001 TYR H 83 ARG 0.001 0.000 ARG J 228 ********************** 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 178 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 1.255 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: 10 residues processed: 178 average time/residue: 1.0086 time to fit residues: 198.4743 Evaluate side-chains 177 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.5905 ------------------------------------------------------------------------------- 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: 0.8980 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105202 restraints weight = 12104.332| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.83 r_work: 0.2970 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11010 Z= 0.230 Angle : 0.504 6.630 15138 Z= 0.284 Chirality : 0.042 0.132 1684 Planarity : 0.003 0.039 1668 Dihedral : 21.249 177.686 1972 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.32 % Allowed : 21.56 % Favored : 77.13 % 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: 0.69 (0.25), residues: 1130 helix: 1.77 (0.22), residues: 496 sheet: 0.40 (0.34), residues: 226 loop : -1.15 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 243 HIS 0.009 0.001 HIS H 171 PHE 0.029 0.001 PHE H 26 TYR 0.011 0.001 TYR H 83 ARG 0.001 0.000 ARG J 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4294.54 seconds wall clock time: 80 minutes 24.24 seconds (4824.24 seconds total)