Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 16:28:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/10_2023/7oug_13076_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/10_2023/7oug_13076.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/10_2023/7oug_13076_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/10_2023/7oug_13076_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/10_2023/7oug_13076_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/10_2023/7oug_13076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/10_2023/7oug_13076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/10_2023/7oug_13076_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oug_13076/10_2023/7oug_13076_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.021 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 76 5.49 5 Mg 4 5.21 5 S 46 5.16 5 C 9424 2.51 5 N 2710 2.21 5 O 2824 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 101": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 276": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 15090 Number of models: 1 Model: "" Number of chains: 16 Chain: "D" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2057 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 2 Chain: "E" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2212 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 257} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2423 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "A" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2057 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 17, 'TRANS': 240} Chain breaks: 2 Chain: "B" Number of atoms: 2212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2212 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 257} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2423 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "K" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "L" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'RLT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'RLT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 239 SG CYS D 35 105.427 119.943 25.979 1.00 64.43 S ATOM 260 SG CYS D 38 103.330 122.249 27.523 1.00 61.41 S ATOM 2296 SG CYS E 35 73.195 55.648 38.011 1.00 18.21 S ATOM 2317 SG CYS E 38 70.364 57.662 38.953 1.00 8.92 S ATOM 7744 SG CYS A 35 22.183 45.021 25.936 1.00 64.00 S ATOM 7765 SG CYS A 38 24.283 42.718 27.481 1.00 58.68 S ATOM 9801 SG CYS B 35 54.346 109.350 37.975 1.00 18.65 S ATOM 9822 SG CYS B 38 57.179 107.339 38.919 1.00 9.34 S Time building chain proxies: 8.56, per 1000 atoms: 0.57 Number of scatterers: 15090 At special positions: 0 Unit cell: (128.7, 166.1, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 46 16.00 P 76 15.00 Mg 4 11.99 F 2 9.00 O 2824 8.00 N 2710 7.00 C 9424 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: 6.19 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" ND1 HIS A 12 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 8 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 38 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 35 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 8 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 35 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 38 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" ND1 HIS D 12 " pdb="ZN ZN D1000 " - pdb=" NE2 HIS D 8 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 38 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 35 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 8 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 35 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 38 " Number of angles added : 6 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 12 sheets defined 46.0% alpha, 10.6% beta 20 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 7.08 Creating SS restraints... Processing helix chain 'D' and resid 4 through 11 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 99 through 113 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 158 through 174 Processing helix chain 'D' and resid 182 through 193 Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'E' and resid 4 through 11 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 25 through 34 Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 130 through 139 removed outlier: 3.511A pdb=" N LEU E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 174 removed outlier: 6.189A pdb=" N LEU E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 193 Processing helix chain 'E' and resid 204 through 208 Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 38 through 49 Processing helix chain 'F' and resid 63 through 82 removed outlier: 3.579A pdb=" N THR F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 102 Proline residue: F 93 - end of helix removed outlier: 3.986A pdb=" N VAL F 96 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 145 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.811A pdb=" N LEU F 170 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 192 removed outlier: 3.885A pdb=" N ARG F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 213 Processing helix chain 'F' and resid 221 through 234 removed outlier: 3.835A pdb=" N GLY F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 249 Processing helix chain 'F' and resid 253 through 256 Processing helix chain 'F' and resid 258 through 275 removed outlier: 4.556A pdb=" N SER F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL F 262 " --> pdb=" O SER F 259 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS F 264 " --> pdb=" O SER F 261 " (cutoff:3.500A) Proline residue: F 265 - end of helix removed outlier: 4.187A pdb=" N LEU F 275 " --> pdb=" O VAL F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 292 removed outlier: 4.112A pdb=" N GLU F 283 " --> pdb=" O THR F 280 " (cutoff:3.500A) Proline residue: F 284 - end of helix removed outlier: 3.618A pdb=" N LEU F 290 " --> pdb=" O MET F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.690A pdb=" N VAL F 302 " --> pdb=" O PRO F 299 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET F 303 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 332 Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 158 through 174 Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.511A pdb=" N LEU B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 174 removed outlier: 6.190A pdb=" N LEU B 156 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 38 through 49 Processing helix chain 'C' and resid 63 through 82 removed outlier: 3.579A pdb=" N THR C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 102 Proline residue: C 93 - end of helix removed outlier: 3.985A pdb=" N VAL C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 161 through 172 removed outlier: 3.811A pdb=" N LEU C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASP C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 3.885A pdb=" N ARG C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 Processing helix chain 'C' and resid 221 through 234 removed outlier: 3.835A pdb=" N GLY C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 258 through 275 removed outlier: 4.555A pdb=" N SER C 261 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 262 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS C 264 " --> pdb=" O SER C 261 " (cutoff:3.500A) Proline residue: C 265 - end of helix removed outlier: 4.187A pdb=" N LEU C 275 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 292 removed outlier: 4.112A pdb=" N GLU C 283 " --> pdb=" O THR C 280 " (cutoff:3.500A) Proline residue: C 284 - end of helix removed outlier: 3.618A pdb=" N LEU C 290 " --> pdb=" O MET C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.690A pdb=" N VAL C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET C 303 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 332 Processing sheet with id= A, first strand: chain 'D' and resid 89 through 94 removed outlier: 7.235A pdb=" N HIS D 118 " --> pdb=" O TRP D 62 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY D 64 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN D 120 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N ILE D 66 " --> pdb=" O ASN D 120 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N ASP D 122 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 14.810A pdb=" N HIS D 68 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG D 142 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N THR D 121 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR D 144 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 245 through 247 Processing sheet with id= C, first strand: chain 'D' and resid 266 through 269 removed outlier: 3.856A pdb=" N GLN D 250 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 89 through 94 removed outlier: 7.081A pdb=" N HIS E 118 " --> pdb=" O TRP E 62 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY E 64 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN E 120 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N ILE E 66 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG E 142 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR E 121 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR E 144 " --> pdb=" O THR E 121 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 230 through 232 Processing sheet with id= F, first strand: chain 'E' and resid 255 through 259 Processing sheet with id= G, first strand: chain 'A' and resid 89 through 94 removed outlier: 7.236A pdb=" N HIS A 118 " --> pdb=" O TRP A 62 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY A 64 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN A 120 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N ILE A 66 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N ASP A 122 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 14.811A pdb=" N HIS A 68 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 142 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR A 121 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR A 144 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 245 through 247 Processing sheet with id= I, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.856A pdb=" N GLN A 250 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 89 through 94 removed outlier: 7.080A pdb=" N HIS B 118 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLY B 64 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN B 120 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N ILE B 66 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG B 142 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR B 121 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR B 144 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 230 through 232 Processing sheet with id= L, first strand: chain 'B' and resid 255 through 259 540 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 4.79 Time building geometry restraints manager: 6.61 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: 3564 1.33 - 1.45: 3583 1.45 - 1.57: 8311 1.57 - 1.69: 152 1.69 - 1.81: 62 Bond restraints: 15672 Sorted by residual: bond pdb=" CAV RLT B 304 " pdb=" NAS RLT B 304 " ideal model delta sigma weight residual 1.450 1.324 0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" CAV RLT E 304 " pdb=" NAS RLT E 304 " ideal model delta sigma weight residual 1.450 1.324 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" CAU RLT E 304 " pdb=" NAR RLT E 304 " ideal model delta sigma weight residual 1.449 1.329 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CAU RLT B 304 " pdb=" NAR RLT B 304 " ideal model delta sigma weight residual 1.449 1.330 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" CBC RLT E 304 " pdb=" NAQ RLT E 304 " ideal model delta sigma weight residual 1.481 1.362 0.119 2.00e-02 2.50e+03 3.52e+01 ... (remaining 15667 not shown) Histogram of bond angle deviations from ideal: 81.93 - 92.34: 4 92.34 - 102.76: 137 102.76 - 113.18: 9465 113.18 - 123.60: 11255 123.60 - 134.02: 817 Bond angle restraints: 21678 Sorted by residual: angle pdb=" CBC RLT B 304 " pdb=" CBF RLT B 304 " pdb=" NAS RLT B 304 " ideal model delta sigma weight residual 109.47 81.93 27.54 3.00e+00 1.11e-01 8.43e+01 angle pdb=" CBC RLT E 304 " pdb=" CBF RLT E 304 " pdb=" NAS RLT E 304 " ideal model delta sigma weight residual 109.47 82.19 27.28 3.00e+00 1.11e-01 8.27e+01 angle pdb=" CAD RLT E 304 " pdb=" CBF RLT E 304 " pdb=" CBC RLT E 304 " ideal model delta sigma weight residual 109.46 89.52 19.94 3.00e+00 1.11e-01 4.42e+01 angle pdb=" CAD RLT B 304 " pdb=" CBF RLT B 304 " pdb=" CBC RLT B 304 " ideal model delta sigma weight residual 109.46 89.57 19.89 3.00e+00 1.11e-01 4.40e+01 angle pdb=" CAA RLT E 304 " pdb=" CAW RLT E 304 " pdb=" OAT RLT E 304 " ideal model delta sigma weight residual 134.90 115.25 19.65 3.00e+00 1.11e-01 4.29e+01 ... (remaining 21673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 7621 15.99 - 31.98: 839 31.98 - 47.97: 365 47.97 - 63.96: 175 63.96 - 79.95: 20 Dihedral angle restraints: 9020 sinusoidal: 4104 harmonic: 4916 Sorted by residual: dihedral pdb=" CA TYR E 230 " pdb=" C TYR E 230 " pdb=" N TYR E 231 " pdb=" CA TYR E 231 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 230 " pdb=" C TYR B 230 " pdb=" N TYR B 231 " pdb=" CA TYR B 231 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR D 230 " pdb=" C TYR D 230 " pdb=" N TYR D 231 " pdb=" CA TYR D 231 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 9017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1790 0.037 - 0.074: 432 0.074 - 0.110: 142 0.110 - 0.147: 40 0.147 - 0.184: 2 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CG LEU B 257 " pdb=" CB LEU B 257 " pdb=" CD1 LEU B 257 " pdb=" CD2 LEU B 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CG LEU E 257 " pdb=" CB LEU E 257 " pdb=" CD1 LEU E 257 " pdb=" CD2 LEU E 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CA ILE E 147 " pdb=" N ILE E 147 " pdb=" C ILE E 147 " pdb=" CB ILE E 147 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2403 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAV RLT E 304 " 0.081 2.00e-02 2.50e+03 2.61e-01 8.52e+02 pdb=" CBA RLT E 304 " -0.176 2.00e-02 2.50e+03 pdb=" CBF RLT E 304 " -0.307 2.00e-02 2.50e+03 pdb=" NAS RLT E 304 " 0.455 2.00e-02 2.50e+03 pdb=" OAF RLT E 304 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAV RLT B 304 " 0.080 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" CBA RLT B 304 " -0.175 2.00e-02 2.50e+03 pdb=" CBF RLT B 304 " -0.305 2.00e-02 2.50e+03 pdb=" NAS RLT B 304 " 0.452 2.00e-02 2.50e+03 pdb=" OAF RLT B 304 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAN RLT B 304 " -0.158 2.00e-02 2.50e+03 1.30e-01 2.10e+02 pdb=" CAU RLT B 304 " 0.052 2.00e-02 2.50e+03 pdb=" CBB RLT B 304 " -0.120 2.00e-02 2.50e+03 pdb=" NAR RLT B 304 " 0.204 2.00e-02 2.50e+03 pdb=" OAE RLT B 304 " 0.022 2.00e-02 2.50e+03 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 51 2.39 - 3.02: 8167 3.02 - 3.65: 22423 3.65 - 4.27: 34225 4.27 - 4.90: 55631 Nonbonded interactions: 120497 Sorted by model distance: nonbonded pdb="MG MG B 303 " pdb=" OAE RLT B 304 " model vdw 1.769 2.170 nonbonded pdb=" OE2 GLU B 158 " pdb="MG MG B 303 " model vdw 1.777 2.170 nonbonded pdb=" OE2 GLU E 158 " pdb="MG MG E 303 " model vdw 1.785 2.170 nonbonded pdb="MG MG E 303 " pdb=" OAE RLT E 304 " model vdw 1.786 2.170 nonbonded pdb=" OE1 GLU E 158 " pdb="MG MG E 303 " model vdw 1.833 2.170 ... (remaining 120492 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 3 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 280 or resid 1000)) selection = (chain 'B' and (resid 3 through 39 or resid 52 through 148 or resid 157 through \ 280 or resid 301)) selection = (chain 'D' and (resid 3 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 280 or resid 1000)) selection = (chain 'E' and (resid 3 through 39 or resid 52 through 148 or resid 157 through \ 280 or resid 301)) } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 6.430 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 47.970 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 15672 Z= 0.249 Angle : 0.736 27.544 21678 Z= 0.333 Chirality : 0.039 0.184 2406 Planarity : 0.009 0.261 2466 Dihedral : 17.589 79.953 5808 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.14 % Allowed : 0.07 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.28 (0.20), residues: 1640 helix: 1.16 (0.19), residues: 742 sheet: 0.36 (0.31), residues: 222 loop : -0.94 (0.24), residues: 676 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 477 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 477 average time/residue: 0.3522 time to fit residues: 226.2897 Evaluate side-chains 431 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 50 optimal weight: 0.0570 chunk 80 optimal weight: 0.0870 chunk 98 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS D 195 ASN D 206 GLN D 238 ASN E 21 HIS E 59 ASN E 93 HIS E 241 GLN ** F 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN A 118 HIS A 134 HIS A 195 ASN A 238 ASN B 59 ASN B 123 ASN B 161 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15672 Z= 0.182 Angle : 0.598 13.606 21678 Z= 0.305 Chirality : 0.041 0.163 2406 Planarity : 0.006 0.122 2466 Dihedral : 18.947 82.397 2582 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.92 % Allowed : 12.16 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.12 (0.20), residues: 1640 helix: 0.82 (0.19), residues: 754 sheet: 0.38 (0.32), residues: 222 loop : -0.82 (0.24), residues: 664 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 433 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 443 average time/residue: 0.3651 time to fit residues: 216.8979 Evaluate side-chains 432 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 418 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1646 time to fit residues: 6.0706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 126 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 238 ASN E 59 ASN E 93 HIS E 112 HIS A 238 ASN B 59 ASN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15672 Z= 0.243 Angle : 0.577 11.436 21678 Z= 0.296 Chirality : 0.041 0.153 2406 Planarity : 0.005 0.076 2466 Dihedral : 18.993 85.106 2582 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.85 % Allowed : 13.87 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.11 (0.20), residues: 1640 helix: 0.72 (0.19), residues: 756 sheet: 0.31 (0.31), residues: 242 loop : -0.71 (0.25), residues: 642 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 439 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 445 average time/residue: 0.3577 time to fit residues: 213.2420 Evaluate side-chains 441 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 423 time to evaluate : 1.597 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1905 time to fit residues: 7.6929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 0.0270 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 102 optimal weight: 0.0030 chunk 153 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 63 GLN D 238 ASN E 59 ASN E 112 HIS F 233 ASN F 243 HIS A 238 ASN B 59 ASN C 203 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15672 Z= 0.190 Angle : 0.553 8.353 21678 Z= 0.284 Chirality : 0.039 0.160 2406 Planarity : 0.005 0.065 2466 Dihedral : 18.912 87.300 2582 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.79 % Allowed : 15.45 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.11 (0.20), residues: 1640 helix: 0.65 (0.19), residues: 758 sheet: 0.35 (0.31), residues: 242 loop : -0.61 (0.25), residues: 640 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 425 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 437 average time/residue: 0.3630 time to fit residues: 211.6056 Evaluate side-chains 427 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 416 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1674 time to fit residues: 5.3334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 112 optimal weight: 0.0270 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN D 238 ASN E 59 ASN E 112 HIS F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN B 59 ASN B 112 HIS ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15672 Z= 0.247 Angle : 0.580 8.338 21678 Z= 0.296 Chirality : 0.041 0.200 2406 Planarity : 0.005 0.064 2466 Dihedral : 18.937 88.090 2582 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.65 % Allowed : 17.99 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.01 (0.20), residues: 1640 helix: 0.53 (0.19), residues: 762 sheet: 0.35 (0.31), residues: 242 loop : -0.65 (0.25), residues: 636 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 425 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 436 average time/residue: 0.3718 time to fit residues: 216.8401 Evaluate side-chains 427 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 413 time to evaluate : 1.488 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2056 time to fit residues: 6.8846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.8980 chunk 146 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 162 optimal weight: 0.9990 chunk 134 optimal weight: 0.0000 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN D 238 ASN E 41 ASN E 59 ASN E 112 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 238 ASN B 41 ASN B 59 ASN B 112 HIS C 133 HIS C 203 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15672 Z= 0.189 Angle : 0.577 10.998 21678 Z= 0.292 Chirality : 0.039 0.154 2406 Planarity : 0.005 0.067 2466 Dihedral : 18.888 89.366 2582 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.17 % Allowed : 20.26 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1640 helix: 0.60 (0.19), residues: 758 sheet: 0.37 (0.31), residues: 242 loop : -0.59 (0.25), residues: 640 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 430 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 432 average time/residue: 0.3676 time to fit residues: 212.6861 Evaluate side-chains 426 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 419 time to evaluate : 1.673 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1774 time to fit residues: 4.1987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 0.0870 chunk 118 optimal weight: 0.0050 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.3172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN E 59 ASN E 112 HIS E 228 HIS F 203 GLN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 238 ASN B 59 ASN B 112 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15672 Z= 0.177 Angle : 0.576 10.853 21678 Z= 0.294 Chirality : 0.039 0.167 2406 Planarity : 0.005 0.061 2466 Dihedral : 18.798 89.757 2582 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.30 % Allowed : 21.22 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1640 helix: 0.63 (0.19), residues: 752 sheet: 0.38 (0.31), residues: 242 loop : -0.51 (0.25), residues: 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 439 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 445 average time/residue: 0.3585 time to fit residues: 213.9837 Evaluate side-chains 440 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 431 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2232 time to fit residues: 5.3179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 ASN E 59 ASN E 112 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 238 ASN B 41 ASN B 59 ASN B 112 HIS B 130 GLN B 134 HIS C 219 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15672 Z= 0.243 Angle : 0.611 11.439 21678 Z= 0.315 Chirality : 0.041 0.160 2406 Planarity : 0.005 0.045 2466 Dihedral : 18.858 89.836 2582 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.30 % Allowed : 21.36 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.07 (0.21), residues: 1640 helix: 0.50 (0.19), residues: 764 sheet: 0.43 (0.31), residues: 242 loop : -0.53 (0.25), residues: 634 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 443 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 446 average time/residue: 0.3798 time to fit residues: 228.6653 Evaluate side-chains 431 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 421 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2000 time to fit residues: 5.3357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 141 optimal weight: 0.0970 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 chunk 136 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 ASN E 59 ASN E 112 HIS F 203 GLN A 238 ASN B 59 ASN B 112 HIS B 134 HIS C 219 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15672 Z= 0.211 Angle : 0.608 12.261 21678 Z= 0.314 Chirality : 0.041 0.167 2406 Planarity : 0.005 0.046 2466 Dihedral : 18.825 89.821 2582 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.37 % Allowed : 21.22 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.06 (0.21), residues: 1640 helix: 0.52 (0.19), residues: 756 sheet: 0.44 (0.31), residues: 242 loop : -0.56 (0.25), residues: 642 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 432 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 435 average time/residue: 0.3703 time to fit residues: 217.2306 Evaluate side-chains 431 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 422 time to evaluate : 1.715 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2083 time to fit residues: 5.3150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 141 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 161 ASN D 238 ASN E 41 ASN E 59 ASN E 112 HIS E 118 HIS A 59 ASN A 238 ASN B 41 ASN B 59 ASN B 60 HIS B 112 HIS B 118 HIS B 134 HIS C 219 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15672 Z= 0.375 Angle : 0.691 12.063 21678 Z= 0.361 Chirality : 0.046 0.233 2406 Planarity : 0.005 0.042 2466 Dihedral : 19.035 89.389 2582 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.82 % Allowed : 22.39 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.27 (0.20), residues: 1640 helix: 0.28 (0.18), residues: 764 sheet: 0.45 (0.31), residues: 242 loop : -0.88 (0.25), residues: 634 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 445 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 448 average time/residue: 0.3710 time to fit residues: 222.0528 Evaluate side-chains 440 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 433 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1904 time to fit residues: 4.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.5980 chunk 122 optimal weight: 0.0770 chunk 19 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 161 ASN D 238 ASN E 59 ASN E 112 HIS F 203 GLN A 238 ASN B 59 ASN B 112 HIS B 118 HIS B 134 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.152390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122571 restraints weight = 22619.163| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.21 r_work: 0.3376 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15672 Z= 0.211 Angle : 0.652 12.536 21678 Z= 0.334 Chirality : 0.042 0.218 2406 Planarity : 0.005 0.049 2466 Dihedral : 18.908 89.214 2582 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.62 % Allowed : 23.56 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.20), residues: 1640 helix: 0.32 (0.19), residues: 760 sheet: 0.42 (0.31), residues: 242 loop : -0.67 (0.25), residues: 638 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4540.24 seconds wall clock time: 82 minutes 8.97 seconds (4928.97 seconds total)