Starting phenix.real_space_refine (version: 1.21rc1) on Sat Sep 30 15:20:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/09_2023/6put_20481.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/09_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_20481/09_2023/6put_20481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/09_2023/6put_20481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/09_2023/6put_20481.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6put_20481/09_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 6.55, per 1000 atoms: 0.60 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: 4.55 Conformation dependent library (CDL) restraints added in 1.3 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: 4.16 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: 3.52 Time building geometry restraints manager: 4.85 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: 2.840 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: 12.360 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 36.500 Find NCS groups from input model: 0.730 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.750 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.223 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: 1.2699 time to fit residues: 327.3752 Evaluate side-chains 182 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2245 time to fit residues: 2.1070 ------------------------------------------------------------------------------- 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** I 222 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 11010 Z= 0.286 Angle : 0.942 24.054 15138 Z= 0.513 Chirality : 0.051 0.344 1684 Planarity : 0.012 0.221 1668 Dihedral : 21.714 155.100 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.71 % Allowed : 4.51 % Favored : 94.78 % 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 : 0.09 % 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: -2.84 (0.21), residues: 1130 helix: -1.49 (0.20), residues: 498 sheet: -1.25 (0.31), residues: 216 loop : -2.55 (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 242 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 1.083 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: 4 residues processed: 225 average time/residue: 1.0405 time to fit residues: 255.9006 Evaluate side-chains 176 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1000 time to fit residues: 1.8385 ------------------------------------------------------------------------------- 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: 0.7980 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 0.0170 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 B 252 GLN G 183 HIS H 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11010 Z= 0.190 Angle : 0.508 5.967 15138 Z= 0.291 Chirality : 0.041 0.136 1684 Planarity : 0.004 0.041 1668 Dihedral : 21.475 176.861 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.82 % Allowed : 16.70 % Favored : 81.48 % 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: -1.28 (0.23), residues: 1130 helix: 0.12 (0.22), residues: 500 sheet: -0.54 (0.33), residues: 226 loop : -2.19 (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: 18 poor density : 185 time to evaluate : 1.199 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: 195 average time/residue: 0.9430 time to fit residues: 200.8154 Evaluate side-chains 181 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 3 residues processed: 8 average time/residue: 0.0849 time to fit residues: 2.4132 ------------------------------------------------------------------------------- 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: 1.9990 chunk 55 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 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: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11010 Z= 0.243 Angle : 0.499 5.648 15138 Z= 0.284 Chirality : 0.042 0.132 1684 Planarity : 0.004 0.043 1668 Dihedral : 21.509 178.781 1896 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 : 3.04 % Allowed : 16.30 % Favored : 80.67 % 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: -0.48 (0.24), residues: 1130 helix: 0.95 (0.22), residues: 500 sheet: -0.39 (0.33), residues: 216 loop : -1.83 (0.28), residues: 414 *********************** 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 203 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.240 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: 30 outliers final: 15 residues processed: 189 average time/residue: 1.0435 time to fit residues: 215.6637 Evaluate side-chains 186 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 6 residues processed: 9 average time/residue: 0.1047 time to fit residues: 3.3707 ------------------------------------------------------------------------------- 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: 0.7980 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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: 0.8789 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11010 Z= 0.316 Angle : 0.529 5.754 15138 Z= 0.300 Chirality : 0.044 0.135 1684 Planarity : 0.004 0.045 1668 Dihedral : 21.577 178.124 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.43 % Allowed : 18.12 % Favored : 79.45 % 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: -0.14 (0.24), residues: 1130 helix: 1.17 (0.22), residues: 498 sheet: -0.20 (0.33), residues: 216 loop : -1.58 (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 195 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 0.836 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: 15 residues processed: 187 average time/residue: 1.0031 time to fit residues: 204.5969 Evaluate side-chains 182 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 8 average time/residue: 0.1101 time to fit residues: 3.1333 ------------------------------------------------------------------------------- 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: 0.0170 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 117 ASN G 216 GLN H 221 GLN ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1949 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= 0.180 Angle : 0.481 5.769 15138 Z= 0.274 Chirality : 0.041 0.133 1684 Planarity : 0.003 0.044 1668 Dihedral : 21.447 179.012 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.42 % Allowed : 20.04 % Favored : 78.54 % 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: 0.24 (0.25), residues: 1130 helix: 1.50 (0.23), residues: 496 sheet: -0.08 (0.33), residues: 216 loop : -1.35 (0.30), residues: 418 *********************** 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 184 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.095 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: 14 outliers final: 8 residues processed: 182 average time/residue: 1.0417 time to fit residues: 207.5562 Evaluate side-chains 176 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0987 time to fit residues: 1.6820 ------------------------------------------------------------------------------- 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: 0.8980 chunk 65 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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: 0.8755 moved from start: 0.2028 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= 0.213 Angle : 0.489 5.594 15138 Z= 0.278 Chirality : 0.042 0.131 1684 Planarity : 0.003 0.041 1668 Dihedral : 21.421 178.562 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.52 % Allowed : 20.75 % Favored : 77.73 % 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: 0.40 (0.25), residues: 1130 helix: 1.62 (0.22), residues: 496 sheet: -0.00 (0.33), residues: 216 loop : -1.23 (0.31), residues: 418 *********************** 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 188 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 173 time to evaluate : 1.179 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: 15 outliers final: 10 residues processed: 186 average time/residue: 1.0639 time to fit residues: 216.5433 Evaluate side-chains 182 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0999 time to fit residues: 1.9977 ------------------------------------------------------------------------------- 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: 0.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2009 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= 0.233 Angle : 0.501 5.672 15138 Z= 0.283 Chirality : 0.042 0.129 1684 Planarity : 0.003 0.039 1668 Dihedral : 21.405 178.454 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.92 % Allowed : 20.45 % Favored : 77.63 % 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: 0.52 (0.25), residues: 1130 helix: 1.65 (0.22), residues: 496 sheet: 0.19 (0.33), residues: 226 loop : -1.19 (0.31), residues: 408 *********************** 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 191 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 1.144 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: 11 residues processed: 187 average time/residue: 1.0934 time to fit residues: 222.5851 Evaluate side-chains 181 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.1154 time to fit residues: 2.1093 ------------------------------------------------------------------------------- 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: 0.7980 chunk 99 optimal weight: 0.4980 chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 H 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11010 Z= 0.191 Angle : 0.495 6.240 15138 Z= 0.280 Chirality : 0.042 0.146 1684 Planarity : 0.003 0.039 1668 Dihedral : 21.396 178.639 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.32 % Allowed : 21.05 % Favored : 77.63 % 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: 0.61 (0.25), residues: 1130 helix: 1.73 (0.22), residues: 496 sheet: 0.23 (0.34), residues: 226 loop : -1.14 (0.31), residues: 408 *********************** 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 185 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 1.271 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: 10 residues processed: 183 average time/residue: 1.0482 time to fit residues: 210.4834 Evaluate side-chains 181 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1053 time to fit residues: 1.7168 ------------------------------------------------------------------------------- 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: 0.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 72 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11010 Z= 0.197 Angle : 0.497 6.619 15138 Z= 0.281 Chirality : 0.042 0.130 1684 Planarity : 0.003 0.039 1668 Dihedral : 21.368 178.757 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.21 % Allowed : 21.56 % Favored : 77.23 % 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: 0.68 (0.25), residues: 1130 helix: 1.79 (0.22), residues: 496 sheet: 0.26 (0.34), residues: 226 loop : -1.12 (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 185 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.145 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: 9 residues processed: 183 average time/residue: 1.0109 time to fit residues: 202.9234 Evaluate side-chains 182 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.1069 time to fit residues: 1.7917 ------------------------------------------------------------------------------- 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: 0.0370 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.139364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106714 restraints weight = 12134.767| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.81 r_work: 0.2997 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2156 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= 0.181 Angle : 0.483 6.544 15138 Z= 0.273 Chirality : 0.041 0.130 1684 Planarity : 0.003 0.039 1668 Dihedral : 21.308 178.899 1896 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.91 % Allowed : 22.06 % Favored : 77.02 % 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: 0.82 (0.25), residues: 1130 helix: 1.92 (0.23), residues: 492 sheet: 0.33 (0.34), residues: 226 loop : -1.04 (0.32), residues: 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4076.32 seconds wall clock time: 73 minutes 1.99 seconds (4381.99 seconds total)