Starting phenix.real_space_refine on Sun Dec 10 17:07:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/12_2023/7ouh_13077_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/12_2023/7ouh_13077.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/12_2023/7ouh_13077_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/12_2023/7ouh_13077_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/12_2023/7ouh_13077_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/12_2023/7ouh_13077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/12_2023/7ouh_13077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/12_2023/7ouh_13077_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ouh_13077/12_2023/7ouh_13077_updated.pdb" } resolution = 3.5 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= 0.024 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 9426 2.51 5 N 2704 2.21 5 O 2822 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "E ASP 174": "OD1" <-> "OD2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 78": "OE1" <-> "OE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15088 Number of models: 1 Model: "" Number of chains: 18 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, 'KLQ': 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, 'KLQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 239 SG CYS D 35 103.581 121.200 24.861 1.00 69.67 S ATOM 260 SG CYS D 38 101.163 123.339 26.815 1.00 63.60 S ATOM 2296 SG CYS E 35 72.912 56.350 37.343 1.00 19.02 S ATOM 2317 SG CYS E 38 70.277 57.163 37.546 1.00 18.08 S ATOM 7744 SG CYS A 35 21.978 43.874 24.439 1.00 67.21 S ATOM 7765 SG CYS A 38 24.387 41.730 26.399 1.00 61.93 S ATOM 9801 SG CYS B 35 52.386 108.733 37.500 1.00 20.30 S ATOM 9822 SG CYS B 38 55.022 107.925 37.718 1.00 18.60 S Time building chain proxies: 8.39, per 1000 atoms: 0.56 Number of scatterers: 15088 At special positions: 0 Unit cell: (126.5, 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 6 9.00 O 2822 8.00 N 2704 7.00 C 9426 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: 6.55 Conformation dependent library (CDL) restraints added in 2.7 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 35 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 38 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 8 " 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 35 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 38 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 8 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 35 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 38 " Number of angles added : 8 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 14 sheets defined 45.2% alpha, 9.9% beta 8 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 6.15 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 112 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 208 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 37 through 40 No H-bonds generated for 'chain 'E' and resid 37 through 40' Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 151 through 174 removed outlier: 5.887A 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 38 through 50 removed outlier: 3.953A pdb=" N CYS F 49 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS F 50 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 80 Processing helix chain 'F' and resid 89 through 102 removed outlier: 3.630A pdb=" N TYR F 92 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Proline residue: F 93 - end of helix Processing helix chain 'F' and resid 131 through 146 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: 3.744A pdb=" N LEU F 170 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 192 removed outlier: 3.954A 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: 3.851A pdb=" N GLY F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 250 Processing helix chain 'F' and resid 253 through 256 Processing helix chain 'F' and resid 260 through 274 removed outlier: 3.791A pdb=" N HIS F 264 " --> pdb=" O SER F 261 " (cutoff:3.500A) Proline residue: F 265 - end of helix Processing helix chain 'F' and resid 279 through 291 removed outlier: 3.652A pdb=" N THR F 282 " --> pdb=" O SER F 279 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU F 283 " --> pdb=" O THR F 280 " (cutoff:3.500A) Proline residue: F 284 - end of helix Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.754A pdb=" N VAL F 302 " --> pdb=" O PRO F 299 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET F 303 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' 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 112 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 208 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 37 through 40 No H-bonds generated for 'chain 'B' and resid 37 through 40' Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 151 through 174 removed outlier: 5.887A 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 38 through 50 removed outlier: 3.953A pdb=" N CYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 80 Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.630A pdb=" N TYR C 92 " --> pdb=" O GLU C 89 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 131 through 146 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: 3.743A pdb=" N LEU C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 3.954A 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: 3.852A pdb=" N GLY C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 253 through 256 Processing helix chain 'C' and resid 260 through 274 removed outlier: 3.792A pdb=" N HIS C 264 " --> pdb=" O SER C 261 " (cutoff:3.500A) Proline residue: C 265 - end of helix Processing helix chain 'C' and resid 279 through 291 removed outlier: 3.653A pdb=" N THR C 282 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU C 283 " --> pdb=" O THR C 280 " (cutoff:3.500A) Proline residue: C 284 - end of helix Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.754A pdb=" N VAL C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET C 303 " --> pdb=" O LYS C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 324 through 332 Processing sheet with id= A, first strand: chain 'D' and resid 62 through 70 Processing sheet with id= B, first strand: chain 'D' and resid 118 through 122 removed outlier: 6.330A pdb=" N ARG D 142 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR D 121 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR D 144 " --> pdb=" O THR D 121 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'D' and resid 230 through 232 Processing sheet with id= D, first strand: chain 'D' and resid 255 through 258 Processing sheet with id= E, first strand: chain 'E' and resid 89 through 94 removed outlier: 7.023A pdb=" N HIS E 118 " --> pdb=" O TRP E 62 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N GLY E 64 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASN E 120 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N ILE E 66 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG E 142 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR E 121 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR E 144 " --> pdb=" O THR E 121 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 230 through 232 Processing sheet with id= G, first strand: chain 'E' and resid 266 through 269 removed outlier: 4.075A pdb=" N GLN E 250 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 62 through 70 Processing sheet with id= I, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.331A pdb=" N ARG A 142 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR A 121 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR A 144 " --> pdb=" O THR A 121 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 230 through 232 Processing sheet with id= K, first strand: chain 'A' and resid 255 through 258 Processing sheet with id= L, first strand: chain 'B' and resid 89 through 94 removed outlier: 7.023A pdb=" N HIS B 118 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N GLY B 64 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN B 120 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N ILE B 66 " --> pdb=" O ASN B 120 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG B 142 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N THR B 121 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR B 144 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 230 through 232 Processing sheet with id= N, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.075A pdb=" N GLN B 250 " --> pdb=" O LEU B 257 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 4.46 Time building geometry restraints manager: 6.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2176 1.31 - 1.43: 4825 1.43 - 1.56: 8451 1.56 - 1.68: 162 1.68 - 1.81: 62 Bond restraints: 15676 Sorted by residual: bond pdb=" CAJ KLQ B 304 " pdb=" CAX KLQ B 304 " ideal model delta sigma weight residual 2.011 1.303 0.708 2.00e-02 2.50e+03 1.25e+03 bond pdb=" CAJ KLQ E 304 " pdb=" CAX KLQ E 304 " ideal model delta sigma weight residual 2.011 1.303 0.708 2.00e-02 2.50e+03 1.25e+03 bond pdb=" CAW KLQ B 304 " pdb=" CBA KLQ B 304 " ideal model delta sigma weight residual 0.990 1.488 -0.498 2.00e-02 2.50e+03 6.19e+02 bond pdb=" CAW KLQ E 304 " pdb=" CBA KLQ E 304 " ideal model delta sigma weight residual 0.990 1.487 -0.497 2.00e-02 2.50e+03 6.19e+02 bond pdb=" CAW KLQ B 304 " pdb=" CAZ KLQ B 304 " ideal model delta sigma weight residual 1.723 1.336 0.387 2.00e-02 2.50e+03 3.74e+02 ... (remaining 15671 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.17: 1014 106.17 - 113.13: 8565 113.13 - 120.10: 5366 120.10 - 127.06: 6298 127.06 - 134.03: 445 Bond angle restraints: 21688 Sorted by residual: angle pdb=" CAY KLQ B 304 " pdb=" CAV KLQ B 304 " pdb=" FAG KLQ B 304 " ideal model delta sigma weight residual 142.84 115.88 26.96 3.00e+00 1.11e-01 8.08e+01 angle pdb=" CAY KLQ E 304 " pdb=" CAV KLQ E 304 " pdb=" FAG KLQ E 304 " ideal model delta sigma weight residual 142.84 115.94 26.90 3.00e+00 1.11e-01 8.04e+01 angle pdb=" CAI KLQ E 304 " pdb=" CAV KLQ E 304 " pdb=" FAG KLQ E 304 " ideal model delta sigma weight residual 97.12 116.37 -19.25 3.00e+00 1.11e-01 4.12e+01 angle pdb=" CAI KLQ B 304 " pdb=" CAV KLQ B 304 " pdb=" FAG KLQ B 304 " ideal model delta sigma weight residual 97.12 116.36 -19.24 3.00e+00 1.11e-01 4.11e+01 angle pdb=" CA PRO C 93 " pdb=" N PRO C 93 " pdb=" CD PRO C 93 " ideal model delta sigma weight residual 112.00 104.52 7.48 1.40e+00 5.10e-01 2.86e+01 ... (remaining 21683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 7753 16.87 - 33.74: 871 33.74 - 50.60: 374 50.60 - 67.47: 96 67.47 - 84.34: 18 Dihedral angle restraints: 9112 sinusoidal: 4196 harmonic: 4916 Sorted by residual: dihedral pdb=" CA PRO F 93 " pdb=" C PRO F 93 " pdb=" N GLU F 94 " pdb=" CA GLU F 94 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA PRO C 93 " pdb=" C PRO C 93 " pdb=" N GLU C 94 " pdb=" CA GLU C 94 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR A 230 " pdb=" C TYR A 230 " pdb=" N TYR A 231 " pdb=" CA TYR A 231 " ideal model delta harmonic sigma weight residual 180.00 161.37 18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 9109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1806 0.035 - 0.071: 426 0.071 - 0.106: 134 0.106 - 0.141: 44 0.141 - 0.176: 2 Chirality restraints: 2412 Sorted by residual: chirality pdb=" CB THR D 11 " pdb=" CA THR D 11 " pdb=" OG1 THR D 11 " pdb=" CG2 THR D 11 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CB THR A 11 " pdb=" CA THR A 11 " pdb=" OG1 THR A 11 " pdb=" CG2 THR A 11 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CBD KLQ B 304 " pdb=" CAO KLQ B 304 " pdb=" NBE KLQ B 304 " pdb=" OAQ KLQ B 304 " both_signs ideal model delta sigma weight residual False 2.53 2.67 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 2409 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 92 " -0.099 5.00e-02 4.00e+02 1.47e-01 3.46e+01 pdb=" N PRO C 93 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 92 " 0.098 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO F 93 " -0.254 5.00e-02 4.00e+02 pdb=" CA PRO F 93 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO F 93 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 124 " 0.047 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO C 125 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.038 5.00e-02 4.00e+02 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 32 2.31 - 2.96: 6475 2.96 - 3.61: 21768 3.61 - 4.25: 34586 4.25 - 4.90: 56331 Nonbonded interactions: 119192 Sorted by model distance: nonbonded pdb="MG MG E 302 " pdb=" OAB KLQ E 304 " model vdw 1.666 2.170 nonbonded pdb="MG MG B 302 " pdb=" OAB KLQ B 304 " model vdw 1.667 2.170 nonbonded pdb=" OE2 GLU B 158 " pdb="MG MG B 303 " model vdw 1.785 2.170 nonbonded pdb=" OE2 GLU E 158 " pdb="MG MG E 303 " model vdw 1.786 2.170 nonbonded pdb=" OE1 GLU E 158 " pdb="MG MG E 303 " model vdw 1.874 2.170 ... (remaining 119187 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 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: 0.020 Extract box with map and model: 6.540 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 48.530 Find NCS groups from input model: 0.970 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 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 : 0.014 0.708 15676 Z= 0.623 Angle : 0.739 26.961 21688 Z= 0.332 Chirality : 0.038 0.176 2412 Planarity : 0.006 0.147 2464 Dihedral : 17.444 84.340 5900 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 0.40 (0.21), residues: 1640 helix: 1.33 (0.20), residues: 748 sheet: -0.18 (0.33), residues: 220 loop : -0.74 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 65 HIS 0.009 0.001 HIS A 209 PHE 0.014 0.001 PHE C 274 TYR 0.011 0.001 TYR C 158 ARG 0.002 0.000 ARG D 142 *********************** 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 557 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 1.696 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 revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.3357 time to fit residues: 257.0493 Evaluate side-chains 504 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1703 ------------------------------------------------------------------------------- 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: 1.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 0.0070 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 HIS D 161 ASN E 123 ASN E 175 ASN E 195 ASN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 HIS ** F 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN B 79 HIS B 192 ASN B 195 ASN B 208 HIS C 44 GLN C 133 HIS ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15676 Z= 0.266 Angle : 0.662 11.523 21688 Z= 0.329 Chirality : 0.042 0.177 2412 Planarity : 0.006 0.073 2464 Dihedral : 19.186 78.487 2674 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.06 % Allowed : 13.12 % Favored : 84.82 % 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: -0.00 (0.20), residues: 1640 helix: 0.76 (0.19), residues: 754 sheet: -0.09 (0.32), residues: 220 loop : -0.76 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 242 HIS 0.017 0.001 HIS E 33 PHE 0.030 0.002 PHE F 246 TYR 0.030 0.002 TYR C 263 ARG 0.007 0.001 ARG A 204 *********************** 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 559 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 529 time to evaluate : 1.550 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: 30 outliers final: 19 residues processed: 536 average time/residue: 0.3452 time to fit residues: 251.5130 Evaluate side-chains 518 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 499 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1525 time to fit residues: 7.3495 ------------------------------------------------------------------------------- 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: 0.0470 chunk 126 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 0.0370 chunk 152 optimal weight: 0.0030 chunk 165 optimal weight: 0.9990 chunk 136 optimal weight: 0.0370 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 0.0170 chunk 122 optimal weight: 1.9990 overall best weight: 0.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN E 59 ASN E 118 HIS E 208 HIS E 266 GLN F 44 GLN F 218 HIS A 161 ASN A 238 ASN B 123 ASN B 192 ASN B 266 GLN C 218 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15676 Z= 0.159 Angle : 0.618 11.677 21688 Z= 0.299 Chirality : 0.039 0.187 2412 Planarity : 0.005 0.054 2464 Dihedral : 18.928 79.131 2674 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.85 % Allowed : 17.86 % Favored : 80.29 % 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: 0.60 (0.19), residues: 752 sheet: 0.04 (0.33), residues: 220 loop : -0.72 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 131 HIS 0.016 0.001 HIS E 33 PHE 0.028 0.002 PHE F 246 TYR 0.014 0.002 TYR E 169 ARG 0.007 0.000 ARG F 70 *********************** 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 525 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 498 time to evaluate : 1.585 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: 27 outliers final: 13 residues processed: 507 average time/residue: 0.3353 time to fit residues: 231.9289 Evaluate side-chains 496 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 483 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2411 time to fit residues: 6.8728 ------------------------------------------------------------------------------- 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: 0.9980 chunk 114 optimal weight: 0.2980 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS E 118 HIS ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 238 ASN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15676 Z= 0.245 Angle : 0.646 11.550 21688 Z= 0.314 Chirality : 0.042 0.368 2412 Planarity : 0.005 0.040 2464 Dihedral : 19.035 78.827 2674 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.85 % Allowed : 19.78 % Favored : 78.37 % 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: -0.18 (0.21), residues: 1640 helix: 0.49 (0.19), residues: 756 sheet: 0.06 (0.31), residues: 240 loop : -0.81 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 205 HIS 0.006 0.001 HIS D 118 PHE 0.025 0.002 PHE C 150 TYR 0.020 0.002 TYR C 158 ARG 0.007 0.001 ARG A 204 *********************** 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 540 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 513 time to evaluate : 1.723 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: 27 outliers final: 18 residues processed: 518 average time/residue: 0.3459 time to fit residues: 244.1623 Evaluate side-chains 514 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 496 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1803 time to fit residues: 7.8595 ------------------------------------------------------------------------------- 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: 0.8980 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 120 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS E 33 HIS E 118 HIS E 134 HIS E 146 HIS ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15676 Z= 0.238 Angle : 0.659 15.755 21688 Z= 0.321 Chirality : 0.042 0.249 2412 Planarity : 0.005 0.037 2464 Dihedral : 19.104 81.960 2674 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.51 % Allowed : 22.12 % Favored : 76.37 % 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: -0.31 (0.21), residues: 1640 helix: 0.29 (0.19), residues: 770 sheet: 0.24 (0.32), residues: 220 loop : -0.85 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 131 HIS 0.010 0.001 HIS D 118 PHE 0.030 0.002 PHE C 99 TYR 0.028 0.002 TYR C 199 ARG 0.009 0.001 ARG C 177 *********************** 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 526 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 504 time to evaluate : 1.648 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: 22 outliers final: 9 residues processed: 512 average time/residue: 0.3384 time to fit residues: 238.5838 Evaluate side-chains 513 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 504 time to evaluate : 1.538 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1758 time to fit residues: 4.8073 ------------------------------------------------------------------------------- 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: 3.9990 chunk 146 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.0000 chunk 40 optimal weight: 0.9990 chunk 162 optimal weight: 0.0070 chunk 134 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS E 134 HIS E 201 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15676 Z= 0.212 Angle : 0.654 12.878 21688 Z= 0.317 Chirality : 0.041 0.269 2412 Planarity : 0.005 0.043 2464 Dihedral : 19.120 84.326 2674 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.24 % Allowed : 23.56 % Favored : 75.21 % 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 (0.21), residues: 1640 helix: 0.32 (0.19), residues: 758 sheet: 0.30 (0.32), residues: 220 loop : -0.82 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 205 HIS 0.008 0.001 HIS F 243 PHE 0.032 0.002 PHE C 99 TYR 0.016 0.002 TYR C 158 ARG 0.012 0.001 ARG C 177 *********************** 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 528 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 510 time to evaluate : 1.560 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: 18 outliers final: 11 residues processed: 515 average time/residue: 0.3502 time to fit residues: 245.6009 Evaluate side-chains 518 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 507 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1848 time to fit residues: 5.6474 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.0020 chunk 90 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS E 118 HIS E 134 HIS ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 HIS A 161 ASN A 209 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN C 217 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15676 Z= 0.208 Angle : 0.658 12.145 21688 Z= 0.319 Chirality : 0.042 0.256 2412 Planarity : 0.004 0.037 2464 Dihedral : 19.107 85.097 2674 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.37 % Allowed : 24.45 % Favored : 74.18 % 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: -0.25 (0.21), residues: 1640 helix: 0.31 (0.19), residues: 764 sheet: 0.33 (0.32), residues: 220 loop : -0.78 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 205 HIS 0.006 0.001 HIS F 243 PHE 0.027 0.002 PHE C 150 TYR 0.015 0.001 TYR C 199 ARG 0.008 0.001 ARG C 177 *********************** 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 531 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 511 time to evaluate : 1.489 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: 20 outliers final: 10 residues processed: 518 average time/residue: 0.3442 time to fit residues: 242.5174 Evaluate side-chains 519 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 509 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1815 time to fit residues: 5.2119 ------------------------------------------------------------------------------- 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: 2.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.2980 chunk 48 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS E 134 HIS ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN A 193 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 123 ASN B 177 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: 0.7225 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15676 Z= 0.201 Angle : 0.674 12.265 21688 Z= 0.324 Chirality : 0.042 0.245 2412 Planarity : 0.005 0.039 2464 Dihedral : 19.082 84.628 2674 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.96 % Allowed : 25.14 % Favored : 73.90 % 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: -0.22 (0.21), residues: 1640 helix: 0.33 (0.19), residues: 762 sheet: 0.39 (0.33), residues: 220 loop : -0.78 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 205 HIS 0.009 0.001 HIS F 243 PHE 0.028 0.002 PHE C 150 TYR 0.014 0.001 TYR C 158 ARG 0.015 0.001 ARG C 177 *********************** 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 520 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 506 time to evaluate : 1.741 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: 14 outliers final: 8 residues processed: 509 average time/residue: 0.3455 time to fit residues: 238.8753 Evaluate side-chains 508 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 500 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1440 time to fit residues: 4.2883 ------------------------------------------------------------------------------- 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: 1.9990 chunk 141 optimal weight: 0.1980 chunk 150 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 0.0270 chunk 142 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 161 ASN D 250 GLN E 118 HIS E 134 HIS F 102 ASN F 206 ASN A 161 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 123 ASN B 201 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15676 Z= 0.191 Angle : 0.676 12.474 21688 Z= 0.326 Chirality : 0.041 0.252 2412 Planarity : 0.004 0.040 2464 Dihedral : 19.048 84.414 2674 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.76 % Allowed : 25.76 % Favored : 73.49 % 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: -0.21 (0.21), residues: 1640 helix: 0.29 (0.19), residues: 764 sheet: 0.46 (0.33), residues: 220 loop : -0.74 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 205 HIS 0.007 0.001 HIS D 118 PHE 0.028 0.002 PHE C 150 TYR 0.025 0.001 TYR C 199 ARG 0.012 0.001 ARG C 177 *********************** 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 521 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 510 time to evaluate : 1.652 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: 11 outliers final: 7 residues processed: 513 average time/residue: 0.3532 time to fit residues: 244.7146 Evaluate side-chains 515 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 508 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1523 time to fit residues: 4.0416 ------------------------------------------------------------------------------- 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: 1.9990 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 105 optimal weight: 0.0470 chunk 141 optimal weight: 2.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 250 GLN E 118 HIS E 134 HIS F 206 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS B 118 HIS B 201 GLN ** 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: 0.7311 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 15676 Z= 0.363 Angle : 0.753 12.013 21688 Z= 0.373 Chirality : 0.047 0.308 2412 Planarity : 0.005 0.048 2464 Dihedral : 19.427 82.599 2674 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.55 % Allowed : 27.06 % Favored : 72.39 % 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: -0.53 (0.20), residues: 1640 helix: 0.08 (0.19), residues: 770 sheet: 0.04 (0.32), residues: 220 loop : -0.88 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 205 HIS 0.008 0.001 HIS A 93 PHE 0.027 0.002 PHE C 150 TYR 0.020 0.002 TYR C 199 ARG 0.011 0.001 ARG D 204 ********************** 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 530 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 522 time to evaluate : 1.622 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: 8 outliers final: 6 residues processed: 522 average time/residue: 0.3497 time to fit residues: 247.8842 Evaluate side-chains 528 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 522 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2821 time to fit residues: 4.7519 ------------------------------------------------------------------------------- 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: 0.0870 chunk 19 optimal weight: 0.0050 chunk 37 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 250 GLN E 118 HIS F 38 GLN A 161 ASN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 118 HIS B 201 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.141652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112721 restraints weight = 25654.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.116507 restraints weight = 11820.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.118846 restraints weight = 7123.244| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15676 Z= 0.206 Angle : 0.723 14.725 21688 Z= 0.349 Chirality : 0.043 0.296 2412 Planarity : 0.005 0.040 2464 Dihedral : 19.224 82.907 2674 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.55 % Allowed : 28.57 % Favored : 70.88 % 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: -0.33 (0.21), residues: 1640 helix: 0.30 (0.19), residues: 750 sheet: 0.12 (0.33), residues: 220 loop : -0.82 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 205 HIS 0.005 0.001 HIS D 118 PHE 0.029 0.002 PHE C 150 TYR 0.022 0.002 TYR C 199 ARG 0.010 0.001 ARG C 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4496.38 seconds wall clock time: 81 minutes 23.20 seconds (4883.20 seconds total)