Starting phenix.real_space_refine (version: dev) on Mon Feb 20 23:49:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/02_2023/7vly_32031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/02_2023/7vly_32031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/02_2023/7vly_32031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/02_2023/7vly_32031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/02_2023/7vly_32031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/02_2023/7vly_32031.pdb" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 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 Process input model Symmetric amino acids flipped Residue "Y GLU 19": "OE1" <-> "OE2" Residue "Y ASP 23": "OD1" <-> "OD2" Residue "Y PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 71": "OD1" <-> "OD2" Residue "Y PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 11": "OD1" <-> "OD2" Residue "Z TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 63": "OE1" <-> "OE2" Residue "Z GLU 83": "OE1" <-> "OE2" Residue "Z ASP 258": "OD1" <-> "OD2" Residue "Z PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 11": "OD1" <-> "OD2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D ASP 258": "OD1" <-> "OD2" Residue "E TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F ASP 23": "OD1" <-> "OD2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G GLU 247": "OE1" <-> "OE2" Residue "H ASP 17": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13347 Number of models: 1 Model: "" Number of chains: 18 Chain: "Y" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1773 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain: "Z" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2307 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain: "A" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 347 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'TRANS': 46} Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1773 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2307 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain: "E" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 347 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'TRANS': 46} Chain: "F" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1773 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain: "G" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2307 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain: "H" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 347 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'TRANS': 46} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 8.10, per 1000 atoms: 0.61 Number of scatterers: 13347 At special positions: 0 Unit cell: (128.182, 120.592, 105.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2337 8.00 N 2217 7.00 C 8706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 14 " distance=2.03 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 14 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 44 " distance=2.03 Simple disulfide: pdb=" SG CYS H 9 " - pdb=" SG CYS H 14 " distance=2.03 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 44 " distance=2.03 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: 5.81 Conformation dependent library (CDL) restraints added in 2.1 seconds 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3162 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 3 sheets defined 74.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'Y' and resid 2 through 23 removed outlier: 3.861A pdb=" N ILE Y 21 " --> pdb=" O GLY Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 40 removed outlier: 4.420A pdb=" N THR Y 35 " --> pdb=" O LEU Y 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL Y 40 " --> pdb=" O LEU Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 58 Processing helix chain 'Y' and resid 71 through 85 removed outlier: 4.090A pdb=" N ALA Y 75 " --> pdb=" O ASP Y 71 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA Y 80 " --> pdb=" O SER Y 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 131 removed outlier: 3.859A pdb=" N ILE Y 101 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) Proline residue: Y 102 - end of helix removed outlier: 4.179A pdb=" N VAL Y 119 " --> pdb=" O ARG Y 115 " (cutoff:3.500A) Proline residue: Y 120 - end of helix Processing helix chain 'Y' and resid 133 through 161 removed outlier: 4.127A pdb=" N VAL Y 137 " --> pdb=" O ASN Y 133 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU Y 138 " --> pdb=" O ILE Y 134 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE Y 152 " --> pdb=" O GLN Y 148 " (cutoff:3.500A) Proline residue: Y 155 - end of helix removed outlier: 3.952A pdb=" N PHE Y 161 " --> pdb=" O ALA Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 166 through 173 Processing helix chain 'Y' and resid 175 through 187 removed outlier: 3.624A pdb=" N GLY Y 187 " --> pdb=" O ALA Y 183 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 201 removed outlier: 4.138A pdb=" N VAL Y 192 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY Y 193 " --> pdb=" O VAL Y 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL Y 197 " --> pdb=" O GLY Y 193 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 217 Processing helix chain 'Y' and resid 223 through 246 removed outlier: 3.622A pdb=" N MET Y 244 " --> pdb=" O ASN Y 240 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY Y 245 " --> pdb=" O LEU Y 241 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY Y 246 " --> pdb=" O SER Y 242 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 19 Processing helix chain 'Z' and resid 20 through 22 No H-bonds generated for 'chain 'Z' and resid 20 through 22' Processing helix chain 'Z' and resid 32 through 40 Processing helix chain 'Z' and resid 40 through 48 Processing helix chain 'Z' and resid 52 through 62 Processing helix chain 'Z' and resid 68 through 70 No H-bonds generated for 'chain 'Z' and resid 68 through 70' Processing helix chain 'Z' and resid 71 through 89 removed outlier: 4.473A pdb=" N ILE Z 75 " --> pdb=" O ILE Z 71 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 96 through 117 removed outlier: 4.079A pdb=" N LYS Z 101 " --> pdb=" O ILE Z 97 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL Z 102 " --> pdb=" O GLN Z 98 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY Z 106 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) Proline residue: Z 107 - end of helix Proline residue: Z 114 - end of helix Processing helix chain 'Z' and resid 119 through 133 removed outlier: 3.859A pdb=" N MET Z 123 " --> pdb=" O THR Z 119 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU Z 131 " --> pdb=" O LEU Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 137 through 165 Processing helix chain 'Z' and resid 165 through 171 removed outlier: 3.564A pdb=" N ILE Z 169 " --> pdb=" O ALA Z 165 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR Z 170 " --> pdb=" O GLY Z 166 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP Z 171 " --> pdb=" O SER Z 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 165 through 171' Processing helix chain 'Z' and resid 175 through 201 removed outlier: 3.666A pdb=" N VAL Z 201 " --> pdb=" O VAL Z 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 230 through 241 Processing helix chain 'Z' and resid 253 through 261 removed outlier: 3.570A pdb=" N LEU Z 260 " --> pdb=" O ASN Z 256 " (cutoff:3.500A) Processing helix chain 'Z' and resid 263 through 279 Processing helix chain 'Z' and resid 282 through 300 Processing helix chain 'A' and resid 17 through 36 Processing helix chain 'C' and resid 2 through 23 removed outlier: 3.954A pdb=" N ILE C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 40 removed outlier: 4.421A pdb=" N THR C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 Processing helix chain 'C' and resid 71 through 85 removed outlier: 4.069A pdb=" N ALA C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 130 removed outlier: 3.882A pdb=" N ILE C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) Proline residue: C 102 - end of helix removed outlier: 4.091A pdb=" N VAL C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) Proline residue: C 120 - end of helix Processing helix chain 'C' and resid 133 through 161 removed outlier: 4.174A pdb=" N VAL C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 138 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) Proline residue: C 155 - end of helix removed outlier: 3.948A pdb=" N PHE C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.663A pdb=" N GLY C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 removed outlier: 4.100A pdb=" N VAL C 192 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 223 through 243 removed outlier: 3.512A pdb=" N LYS C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 32 through 40 Processing helix chain 'D' and resid 40 through 48 Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 71 through 89 removed outlier: 4.519A pdb=" N ILE D 75 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 117 removed outlier: 4.098A pdb=" N LYS D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Proline residue: D 107 - end of helix Proline residue: D 114 - end of helix Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.717A pdb=" N MET D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 165 Processing helix chain 'D' and resid 165 through 171 removed outlier: 3.667A pdb=" N ILE D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 165 through 171' Processing helix chain 'D' and resid 175 through 201 removed outlier: 3.644A pdb=" N VAL D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'D' and resid 253 through 261 removed outlier: 3.556A pdb=" N LEU D 260 " --> pdb=" O ASN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 279 Processing helix chain 'D' and resid 282 through 300 Processing helix chain 'E' and resid 17 through 36 Processing helix chain 'F' and resid 2 through 23 removed outlier: 3.940A pdb=" N ILE F 21 " --> pdb=" O GLY F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 40 removed outlier: 4.408A pdb=" N THR F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 58 Processing helix chain 'F' and resid 71 through 85 removed outlier: 4.071A pdb=" N ALA F 75 " --> pdb=" O ASP F 71 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 130 removed outlier: 3.873A pdb=" N ILE F 101 " --> pdb=" O ILE F 97 " (cutoff:3.500A) Proline residue: F 102 - end of helix removed outlier: 4.128A pdb=" N VAL F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Proline residue: F 120 - end of helix Processing helix chain 'F' and resid 133 through 161 removed outlier: 4.146A pdb=" N VAL F 137 " --> pdb=" O ASN F 133 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Proline residue: F 155 - end of helix removed outlier: 3.932A pdb=" N PHE F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 Processing helix chain 'F' and resid 175 through 187 removed outlier: 3.651A pdb=" N GLY F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 201 removed outlier: 4.134A pdb=" N VAL F 192 " --> pdb=" O MET F 188 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY F 193 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 197 " --> pdb=" O GLY F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 217 Processing helix chain 'F' and resid 223 through 243 Processing helix chain 'G' and resid 8 through 19 Processing helix chain 'G' and resid 20 through 22 No H-bonds generated for 'chain 'G' and resid 20 through 22' Processing helix chain 'G' and resid 32 through 40 Processing helix chain 'G' and resid 40 through 48 Processing helix chain 'G' and resid 52 through 62 Processing helix chain 'G' and resid 71 through 89 removed outlier: 4.511A pdb=" N ILE G 75 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.504A pdb=" N VAL G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) Proline residue: G 107 - end of helix Proline residue: G 114 - end of helix Processing helix chain 'G' and resid 119 through 133 removed outlier: 3.918A pdb=" N MET G 123 " --> pdb=" O THR G 119 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 165 Processing helix chain 'G' and resid 165 through 171 removed outlier: 3.658A pdb=" N ILE G 169 " --> pdb=" O ALA G 165 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR G 170 " --> pdb=" O GLY G 166 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP G 171 " --> pdb=" O SER G 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 165 through 171' Processing helix chain 'G' and resid 175 through 201 removed outlier: 3.636A pdb=" N VAL G 201 " --> pdb=" O VAL G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 241 Processing helix chain 'G' and resid 253 through 261 removed outlier: 3.615A pdb=" N LEU G 260 " --> pdb=" O ASN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 279 Processing helix chain 'G' and resid 282 through 300 Processing helix chain 'H' and resid 17 through 36 Processing sheet with id=AA1, first strand: chain 'Z' and resid 208 through 210 Processing sheet with id=AA2, first strand: chain 'D' and resid 208 through 210 Processing sheet with id=AA3, first strand: chain 'G' and resid 208 through 210 880 hydrogen bonds defined for protein. 2631 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4182 1.34 - 1.46: 3071 1.46 - 1.58: 6196 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 13599 Sorted by residual: bond pdb=" C ALA D 206 " pdb=" N PRO D 207 " ideal model delta sigma weight residual 1.333 1.352 -0.019 1.20e-02 6.94e+03 2.63e+00 bond pdb=" C ALA G 206 " pdb=" N PRO G 207 " ideal model delta sigma weight residual 1.333 1.352 -0.019 1.20e-02 6.94e+03 2.54e+00 bond pdb=" CB LYS G 164 " pdb=" CG LYS G 164 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" C ARG D 121 " pdb=" O ARG D 121 " ideal model delta sigma weight residual 1.244 1.234 0.010 1.00e-02 1.00e+04 9.77e-01 bond pdb=" C ARG G 121 " pdb=" O ARG G 121 " ideal model delta sigma weight residual 1.244 1.234 0.010 1.00e-02 1.00e+04 9.45e-01 ... (remaining 13594 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.25: 472 107.25 - 114.01: 7977 114.01 - 120.77: 5912 120.77 - 127.53: 3945 127.53 - 134.30: 180 Bond angle restraints: 18486 Sorted by residual: angle pdb=" C LYS Z 49 " pdb=" N THR Z 50 " pdb=" CA THR Z 50 " ideal model delta sigma weight residual 121.71 115.21 6.50 1.39e+00 5.18e-01 2.18e+01 angle pdb=" C LYS G 49 " pdb=" N THR G 50 " pdb=" CA THR G 50 " ideal model delta sigma weight residual 121.71 115.28 6.43 1.39e+00 5.18e-01 2.14e+01 angle pdb=" C LYS D 49 " pdb=" N THR D 50 " pdb=" CA THR D 50 " ideal model delta sigma weight residual 121.71 115.36 6.35 1.39e+00 5.18e-01 2.09e+01 angle pdb=" CA LYS G 164 " pdb=" CB LYS G 164 " pdb=" CG LYS G 164 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.62e+01 angle pdb=" C PHE Z 205 " pdb=" N ALA Z 206 " pdb=" CA ALA Z 206 " ideal model delta sigma weight residual 122.28 118.79 3.49 1.02e+00 9.61e-01 1.17e+01 ... (remaining 18481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 7049 18.64 - 37.28: 697 37.28 - 55.92: 147 55.92 - 74.55: 28 74.55 - 93.19: 20 Dihedral angle restraints: 7941 sinusoidal: 2985 harmonic: 4956 Sorted by residual: dihedral pdb=" CA LYS D 51 " pdb=" C LYS D 51 " pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta harmonic sigma weight residual 180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA LYS G 51 " pdb=" C LYS G 51 " pdb=" N GLU G 52 " pdb=" CA GLU G 52 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LYS Z 51 " pdb=" C LYS Z 51 " pdb=" N GLU Z 52 " pdb=" CA GLU Z 52 " ideal model delta harmonic sigma weight residual -180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 7938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1243 0.025 - 0.051: 504 0.051 - 0.076: 312 0.076 - 0.102: 111 0.102 - 0.127: 35 Chirality restraints: 2205 Sorted by residual: chirality pdb=" CA ILE C 162 " pdb=" N ILE C 162 " pdb=" C ILE C 162 " pdb=" CB ILE C 162 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE Y 162 " pdb=" N ILE Y 162 " pdb=" C ILE Y 162 " pdb=" CB ILE Y 162 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE F 162 " pdb=" N ILE F 162 " pdb=" C ILE F 162 " pdb=" CB ILE F 162 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 2202 not shown) Planarity restraints: 2274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 69 " -0.050 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO C 70 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 70 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 70 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA Y 69 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO Y 70 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO Y 70 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Y 70 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 69 " 0.049 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO F 70 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 70 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 70 " 0.041 5.00e-02 4.00e+02 ... (remaining 2271 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2281 2.77 - 3.30: 13273 3.30 - 3.83: 23862 3.83 - 4.37: 26955 4.37 - 4.90: 45800 Nonbonded interactions: 112171 Sorted by model distance: nonbonded pdb=" OE2 GLU Y 205 " pdb=" NZ LYS Z 183 " model vdw 2.232 2.520 nonbonded pdb=" O ALA Y 72 " pdb=" OG SER Y 76 " model vdw 2.234 2.440 nonbonded pdb=" OD2 ASP G 113 " pdb=" O6 MAN G 401 " model vdw 2.241 2.440 nonbonded pdb=" OD2 ASP D 113 " pdb=" O6 MAN D 401 " model vdw 2.254 2.440 nonbonded pdb=" OD2 ASP Z 113 " pdb=" O6 MAN Z 401 " model vdw 2.255 2.440 ... (remaining 112166 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' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'Y' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 8706 2.51 5 N 2217 2.21 5 O 2337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 5.080 Check model and map are aligned: 0.200 Process input model: 36.730 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 : 0.002 0.036 13599 Z= 0.155 Angle : 0.599 8.460 18486 Z= 0.344 Chirality : 0.040 0.127 2205 Planarity : 0.005 0.077 2274 Dihedral : 16.106 93.193 4761 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.21), residues: 1755 helix: 1.66 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 510 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 245 time to evaluate : 1.611 Fit side-chains outliers start: 34 outliers final: 16 residues processed: 271 average time/residue: 1.1218 time to fit residues: 335.1967 Evaluate side-chains 247 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 231 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.1146 time to fit residues: 2.6700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.5980 chunk 129 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 0.0020 chunk 51 optimal weight: 0.0030 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 238 GLN D 98 GLN D 148 ASN D 159 GLN D 179 GLN D 204 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 13599 Z= 0.152 Angle : 0.532 7.260 18486 Z= 0.273 Chirality : 0.040 0.121 2205 Planarity : 0.005 0.070 2274 Dihedral : 6.544 93.290 1875 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.20), residues: 1755 helix: 2.20 (0.15), residues: 1242 sheet: None (None), residues: 0 loop : -1.65 (0.26), residues: 513 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 244 time to evaluate : 1.479 Fit side-chains outliers start: 54 outliers final: 19 residues processed: 280 average time/residue: 1.0764 time to fit residues: 332.6832 Evaluate side-chains 254 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 235 time to evaluate : 1.520 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 0.4168 time to fit residues: 4.6356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 138 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 238 GLN D 98 GLN D 159 GLN D 204 GLN G 237 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13599 Z= 0.195 Angle : 0.551 8.634 18486 Z= 0.283 Chirality : 0.042 0.133 2205 Planarity : 0.005 0.072 2274 Dihedral : 6.668 92.733 1875 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 3.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.77 (0.21), residues: 1755 helix: 2.27 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.75 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 1.487 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 27 residues processed: 280 average time/residue: 1.1156 time to fit residues: 343.9174 Evaluate side-chains 269 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 242 time to evaluate : 1.441 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 22 residues processed: 5 average time/residue: 0.3588 time to fit residues: 4.2375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 238 GLN D 98 GLN D 159 GLN D 179 GLN D 204 GLN F 240 ASN G 237 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13599 Z= 0.210 Angle : 0.566 12.388 18486 Z= 0.288 Chirality : 0.042 0.136 2205 Planarity : 0.005 0.073 2274 Dihedral : 6.726 91.690 1875 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.21), residues: 1755 helix: 2.26 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.81 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 242 time to evaluate : 1.537 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 32 residues processed: 271 average time/residue: 1.0898 time to fit residues: 326.0850 Evaluate side-chains 265 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 233 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 23 residues processed: 9 average time/residue: 0.5190 time to fit residues: 7.5862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.3980 chunk 148 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 238 GLN C 168 GLN D 98 GLN D 159 GLN D 179 GLN D 204 GLN F 240 ASN G 238 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13599 Z= 0.182 Angle : 0.543 12.293 18486 Z= 0.276 Chirality : 0.041 0.129 2205 Planarity : 0.005 0.071 2274 Dihedral : 6.691 91.689 1875 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.83 (0.21), residues: 1755 helix: 2.34 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 239 time to evaluate : 1.483 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 28 residues processed: 268 average time/residue: 1.0557 time to fit residues: 312.9057 Evaluate side-chains 264 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 6 average time/residue: 0.4058 time to fit residues: 5.1849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.5980 chunk 148 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 238 GLN C 168 GLN D 98 GLN D 159 GLN D 179 GLN D 204 GLN F 240 ASN G 238 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 13599 Z= 0.159 Angle : 0.536 12.377 18486 Z= 0.269 Chirality : 0.040 0.123 2205 Planarity : 0.005 0.070 2274 Dihedral : 6.622 92.036 1875 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.21), residues: 1755 helix: 2.47 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 241 time to evaluate : 1.603 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 27 residues processed: 270 average time/residue: 1.0802 time to fit residues: 322.9219 Evaluate side-chains 263 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 236 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 5 average time/residue: 0.1600 time to fit residues: 3.4781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 92 optimal weight: 0.0670 chunk 164 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 238 GLN C 168 GLN D 98 GLN D 179 GLN D 204 GLN F 240 ASN G 238 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 13599 Z= 0.162 Angle : 0.541 12.645 18486 Z= 0.271 Chirality : 0.040 0.127 2205 Planarity : 0.005 0.070 2274 Dihedral : 6.605 92.478 1875 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.99 (0.21), residues: 1755 helix: 2.48 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 235 time to evaluate : 1.570 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 28 residues processed: 262 average time/residue: 1.0770 time to fit residues: 315.4194 Evaluate side-chains 260 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 5 average time/residue: 0.3627 time to fit residues: 4.2890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN D 98 GLN D 204 GLN F 240 ASN G 237 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13599 Z= 0.177 Angle : 0.556 12.677 18486 Z= 0.278 Chirality : 0.041 0.127 2205 Planarity : 0.005 0.070 2274 Dihedral : 6.633 92.608 1875 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.21), residues: 1755 helix: 2.44 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 1.573 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 27 residues processed: 258 average time/residue: 1.1075 time to fit residues: 315.6740 Evaluate side-chains 258 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 231 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 4 average time/residue: 0.4789 time to fit residues: 4.2014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 47 optimal weight: 0.0370 chunk 138 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN D 98 GLN D 204 GLN F 148 GLN F 240 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 13599 Z= 0.157 Angle : 0.543 12.791 18486 Z= 0.272 Chirality : 0.040 0.127 2205 Planarity : 0.005 0.070 2274 Dihedral : 6.582 92.683 1875 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.21), residues: 1755 helix: 2.53 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 235 time to evaluate : 1.476 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 25 residues processed: 261 average time/residue: 1.0565 time to fit residues: 305.3376 Evaluate side-chains 254 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 229 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 2 average time/residue: 0.1768 time to fit residues: 2.5742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 83 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN D 98 GLN D 204 GLN F 148 GLN F 240 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13599 Z= 0.206 Angle : 0.577 12.876 18486 Z= 0.290 Chirality : 0.042 0.147 2205 Planarity : 0.005 0.072 2274 Dihedral : 6.694 92.642 1875 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.92 (0.21), residues: 1755 helix: 2.40 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 233 time to evaluate : 1.606 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 24 residues processed: 258 average time/residue: 1.1069 time to fit residues: 315.2822 Evaluate side-chains 256 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 232 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 1 average time/residue: 0.1520 time to fit residues: 2.2249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 0.0270 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN D 98 GLN D 204 GLN F 240 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.174626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140444 restraints weight = 13596.481| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.79 r_work: 0.3421 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13599 Z= 0.198 Angle : 0.573 12.999 18486 Z= 0.288 Chirality : 0.042 0.142 2205 Planarity : 0.005 0.071 2274 Dihedral : 6.704 91.904 1875 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.21), residues: 1755 helix: 2.38 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.79 (0.26), residues: 504 =============================================================================== Job complete usr+sys time: 5363.82 seconds wall clock time: 95 minutes 21.35 seconds (5721.35 seconds total)