Starting phenix.real_space_refine on Wed Sep 25 14:14:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k26_36829/09_2024/8k26_36829.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k26_36829/09_2024/8k26_36829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k26_36829/09_2024/8k26_36829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k26_36829/09_2024/8k26_36829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k26_36829/09_2024/8k26_36829.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k26_36829/09_2024/8k26_36829.cif" } resolution = 3.6 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= 0.002 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6722 2.51 5 N 1815 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10549 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 2292 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2282 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 289, 2282 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 2314 Chain: "E" Number of atoms: 2343 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2335 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 295, 2335 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 2375 Chain: "d" Number of atoms: 2296 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2291 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 289, 2286 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 2326 Chain: "e" Number of atoms: 2326 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2318 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 295, 2318 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 2358 Chain: "A" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 649 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 81} Chain: "a" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 643 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 10.92, per 1000 atoms: 1.04 Number of scatterers: 10549 At special positions: 0 Unit cell: (81.2278, 87.927, 157.431, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1954 8.00 N 1815 7.00 C 6722 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 - 3.00 Amino acid : True - 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: 2.28 Conformation dependent library (CDL) restraints added in 2.3 seconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 54.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.853A pdb=" N ASN D 67 " --> pdb=" O MET D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 109 removed outlier: 4.417A pdb=" N MET D 101 " --> pdb=" O PRO D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 132 removed outlier: 4.282A pdb=" N ARG D 125 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 159 removed outlier: 3.582A pdb=" N ALA D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.628A pdb=" N ALA D 209 " --> pdb=" O GLY D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 4.094A pdb=" N ASP D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 248 removed outlier: 4.019A pdb=" N THR D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.819A pdb=" N LEU D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 280 removed outlier: 3.513A pdb=" N PHE D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN D 279 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.801A pdb=" N LEU D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 110 through 132 Processing helix chain 'E' and resid 142 through 159 Processing helix chain 'E' and resid 161 through 184 Processing helix chain 'E' and resid 196 through 221 Processing helix chain 'E' and resid 236 through 248 removed outlier: 3.847A pdb=" N ILE E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR E 248 " --> pdb=" O ASP E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 264 through 279 Processing helix chain 'E' and resid 280 through 294 removed outlier: 4.112A pdb=" N TYR E 284 " --> pdb=" O ASP E 280 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 10 removed outlier: 3.571A pdb=" N GLN d 9 " --> pdb=" O LEU d 6 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS d 10 " --> pdb=" O THR d 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 6 through 10' Processing helix chain 'd' and resid 57 through 67 removed outlier: 3.542A pdb=" N MET d 61 " --> pdb=" O THR d 57 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN d 67 " --> pdb=" O MET d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 109 removed outlier: 4.411A pdb=" N MET d 101 " --> pdb=" O PRO d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 132 removed outlier: 4.038A pdb=" N ARG d 125 " --> pdb=" O ILE d 121 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL d 126 " --> pdb=" O LEU d 122 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP d 127 " --> pdb=" O LYS d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 144 through 159 removed outlier: 3.574A pdb=" N ALA d 159 " --> pdb=" O GLY d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 167 through 180 removed outlier: 3.803A pdb=" N TYR d 180 " --> pdb=" O LEU d 176 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 183 No H-bonds generated for 'chain 'd' and resid 181 through 183' Processing helix chain 'd' and resid 196 through 220 removed outlier: 3.515A pdb=" N LYS d 200 " --> pdb=" O ASP d 196 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN d 206 " --> pdb=" O LEU d 202 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR d 207 " --> pdb=" O THR d 203 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TYR d 208 " --> pdb=" O LEU d 204 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA d 209 " --> pdb=" O GLY d 205 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA d 219 " --> pdb=" O SER d 215 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU d 220 " --> pdb=" O SER d 216 " (cutoff:3.500A) Processing helix chain 'd' and resid 237 through 261 removed outlier: 4.223A pdb=" N ASP d 241 " --> pdb=" O GLY d 237 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE d 245 " --> pdb=" O ASP d 241 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE d 246 " --> pdb=" O VAL d 242 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR d 248 " --> pdb=" O ASP d 244 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER d 249 " --> pdb=" O ILE d 245 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE d 250 " --> pdb=" O ILE d 246 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU d 252 " --> pdb=" O THR d 248 " (cutoff:3.500A) Proline residue: d 253 - end of helix Processing helix chain 'd' and resid 264 through 279 removed outlier: 3.601A pdb=" N PHE d 268 " --> pdb=" O SER d 264 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN d 279 " --> pdb=" O TYR d 275 " (cutoff:3.500A) Processing helix chain 'd' and resid 280 through 294 removed outlier: 3.623A pdb=" N ARG d 291 " --> pdb=" O ASN d 287 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU d 292 " --> pdb=" O ASN d 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 65 Processing helix chain 'e' and resid 98 through 110 removed outlier: 3.656A pdb=" N GLN e 102 " --> pdb=" O THR e 98 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP e 110 " --> pdb=" O ARG e 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 132 Processing helix chain 'e' and resid 142 through 159 Processing helix chain 'e' and resid 161 through 184 Processing helix chain 'e' and resid 196 through 221 Processing helix chain 'e' and resid 236 through 248 removed outlier: 3.558A pdb=" N PHE e 240 " --> pdb=" O GLY e 236 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE e 245 " --> pdb=" O ASP e 241 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE e 246 " --> pdb=" O VAL e 242 " (cutoff:3.500A) Processing helix chain 'e' and resid 250 through 262 Processing helix chain 'e' and resid 264 through 279 Processing helix chain 'e' and resid 280 through 295 removed outlier: 4.149A pdb=" N MET e 294 " --> pdb=" O LYS e 290 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU e 295 " --> pdb=" O ARG e 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.534A pdb=" N GLY A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 23 removed outlier: 3.683A pdb=" N ALA a 23 " --> pdb=" O ARG a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 53 removed outlier: 4.041A pdb=" N GLY a 53 " --> pdb=" O LEU a 49 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 16 removed outlier: 5.828A pdb=" N ASN D 12 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE D 47 " --> pdb=" O ASN D 12 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR D 14 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D 71 " --> pdb=" O HIS D 89 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE E 48 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR E 74 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU E 50 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN E 12 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLY E 49 " --> pdb=" O ASN E 12 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR E 14 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 20 through 24 Processing sheet with id=AA3, first strand: chain 'D' and resid 55 through 56 removed outlier: 3.638A pdb=" N ILE D 56 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 56 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL E 23 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 15 through 16 removed outlier: 3.790A pdb=" N VAL d 71 " --> pdb=" O HIS d 89 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASN e 12 " --> pdb=" O PHE e 47 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLY e 49 " --> pdb=" O ASN e 12 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR e 14 " --> pdb=" O GLY e 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 27 through 31 removed outlier: 3.814A pdb=" N ILE d 56 " --> pdb=" O ILE e 56 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE e 56 " --> pdb=" O ILE d 56 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL e 23 " --> pdb=" O THR e 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.695A pdb=" N GLU A 26 " --> pdb=" O GLU A 34 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 34 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE A 68 " --> pdb=" O CYS A 60 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 62 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL A 66 " --> pdb=" O TYR A 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 26 through 27 removed outlier: 3.662A pdb=" N GLU a 26 " --> pdb=" O GLU a 34 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU a 34 " --> pdb=" O GLU a 26 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE a 68 " --> pdb=" O CYS a 60 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR a 62 " --> pdb=" O VAL a 66 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL a 66 " --> pdb=" O TYR a 62 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 2.70 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: 2209 1.33 - 1.45: 2537 1.45 - 1.57: 5923 1.57 - 1.70: 4 1.70 - 1.82: 92 Bond restraints: 10765 Sorted by residual: bond pdb=" CA TRP D 218 " pdb=" C TRP D 218 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.32e-02 5.74e+03 1.78e+01 bond pdb=" CA PHE D 226 " pdb=" C PHE D 226 " ideal model delta sigma weight residual 1.523 1.493 0.030 1.00e-02 1.00e+04 8.90e+00 bond pdb=" CB ASN e 279 " pdb=" CG ASN e 279 " ideal model delta sigma weight residual 1.516 1.589 -0.073 2.50e-02 1.60e+03 8.47e+00 bond pdb=" CA MET D 294 " pdb=" CB MET D 294 " ideal model delta sigma weight residual 1.526 1.563 -0.037 1.36e-02 5.41e+03 7.57e+00 bond pdb=" C PHE E 226 " pdb=" N PRO E 227 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.25e-02 6.40e+03 6.19e+00 ... (remaining 10760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 14215 3.85 - 7.70: 278 7.70 - 11.55: 46 11.55 - 15.41: 4 15.41 - 19.26: 2 Bond angle restraints: 14545 Sorted by residual: angle pdb=" N ILE D 222 " pdb=" CA ILE D 222 " pdb=" C ILE D 222 " ideal model delta sigma weight residual 108.36 127.62 -19.26 1.43e+00 4.89e-01 1.81e+02 angle pdb=" N GLY D 221 " pdb=" CA GLY D 221 " pdb=" C GLY D 221 " ideal model delta sigma weight residual 113.18 128.19 -15.01 2.37e+00 1.78e-01 4.01e+01 angle pdb=" CB LYS e 154 " pdb=" CG LYS e 154 " pdb=" CD LYS e 154 " ideal model delta sigma weight residual 111.30 125.47 -14.17 2.30e+00 1.89e-01 3.80e+01 angle pdb=" N GLY d 237 " pdb=" CA GLY d 237 " pdb=" C GLY d 237 " ideal model delta sigma weight residual 111.21 117.26 -6.05 1.04e+00 9.25e-01 3.39e+01 angle pdb=" CA ASN e 279 " pdb=" CB ASN e 279 " pdb=" CG ASN e 279 " ideal model delta sigma weight residual 112.60 118.28 -5.68 1.00e+00 1.00e+00 3.23e+01 ... (remaining 14540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5377 17.73 - 35.45: 820 35.45 - 53.18: 181 53.18 - 70.91: 24 70.91 - 88.64: 16 Dihedral angle restraints: 6418 sinusoidal: 2504 harmonic: 3914 Sorted by residual: dihedral pdb=" CA TYR d 184 " pdb=" C TYR d 184 " pdb=" N GLU d 185 " pdb=" CA GLU d 185 " ideal model delta harmonic sigma weight residual 180.00 -150.87 -29.13 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU d 6 " pdb=" C LEU d 6 " pdb=" N THR d 7 " pdb=" CA THR d 7 " ideal model delta harmonic sigma weight residual -180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA GLN D 261 " pdb=" C GLN D 261 " pdb=" N GLY D 262 " pdb=" CA GLY D 262 " ideal model delta harmonic sigma weight residual 180.00 152.85 27.15 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 6415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1450 0.104 - 0.208: 145 0.208 - 0.312: 18 0.312 - 0.416: 5 0.416 - 0.520: 1 Chirality restraints: 1619 Sorted by residual: chirality pdb=" CA GLN d 4 " pdb=" N GLN d 4 " pdb=" C GLN d 4 " pdb=" CB GLN d 4 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" CA ILE D 222 " pdb=" N ILE D 222 " pdb=" C ILE D 222 " pdb=" CB ILE D 222 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB ILE e 250 " pdb=" CA ILE e 250 " pdb=" CG1 ILE e 250 " pdb=" CG2 ILE e 250 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 1616 not shown) Planarity restraints: 1845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL a 81 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO a 82 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO a 82 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO a 82 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 108 " -0.027 2.00e-02 2.50e+03 2.43e-02 1.48e+01 pdb=" CG TRP E 108 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP E 108 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP E 108 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 108 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 108 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 108 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 108 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 108 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 108 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 104 " -0.023 2.00e-02 2.50e+03 1.86e-02 8.64e+00 pdb=" CG TRP E 104 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP E 104 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP E 104 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 104 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 104 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 104 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 104 " -0.007 2.00e-02 2.50e+03 ... (remaining 1842 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1367 2.76 - 3.29: 10389 3.29 - 3.83: 19229 3.83 - 4.36: 21722 4.36 - 4.90: 35948 Nonbonded interactions: 88655 Sorted by model distance: nonbonded pdb=" OD1 ASP d 135 " pdb=" OH TYR d 275 " model vdw 2.221 3.040 nonbonded pdb=" NE2 GLN D 9 " pdb=" OE1 GLN a 40 " model vdw 2.233 3.120 nonbonded pdb=" OE1 GLN e 27 " pdb=" OG1 THR e 39 " model vdw 2.261 3.040 nonbonded pdb=" O TYR e 79 " pdb=" OG SER e 215 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLN D 27 " pdb=" OG SER a 22 " model vdw 2.282 3.040 ... (remaining 88650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 84)) selection = chain 'a' } ncs_group { reference = (chain 'D' and (resid 1 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 105 or (resid 107 and (name N or \ name CA or name C or name O or name CB )) or resid 108 through 113 or (resid 11 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 115 through \ 123 or (resid 124 and (name N or name CA or name C or name O or name CB )) or re \ sid 125 through 128 or (resid 129 and (name N or name CA or name C or name O or \ name CB )) or resid 130 through 149 or resid 151 or (resid 152 through 153 and ( \ name N or name CA or name C or name O or name CB )) or resid 154 through 161 or \ (resid 162 and (name N or name CA or name C or name O or name CB )) or resid 163 \ through 165 or (resid 166 and (name N or name CA or name C or name O or name CB \ )) or resid 167 through 192 or (resid 193 and (name N or name CA or name C or n \ ame O or name CB )) or resid 194 through 227 or (resid 228 and (name N or name C \ A or name C or name O or name CB )) or resid 229 through 276 or (resid 277 throu \ gh 278 and (name N or name CA or name C or name O or name CB )) or resid 279 thr \ ough 281 or (resid 282 through 283 and (name N or name CA or name C or name O or \ name CB )) or resid 284 through 285 or (resid 286 and (name N or name CA or nam \ e C or name O or name CB )) or resid 288 through 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 through 295)) selection = (chain 'E' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 15 or (resid 16 and (name N or name CA \ or name C or name O or name CB )) or resid 17 through 75 or resid 83 through 10 \ 5 or resid 107 through 113 or (resid 114 and (name N or name CA or name C or nam \ e O or name CB )) or resid 115 through 128 or (resid 129 and (name N or name CA \ or name C or name O or name CB )) or resid 130 through 149 or resid 151 or (resi \ d 152 through 153 and (name N or name CA or name C or name O or name CB )) or re \ sid 154 through 165 or (resid 166 and (name N or name CA or name C or name O or \ name CB )) or resid 167 through 192 or (resid 193 and (name N or name CA or name \ C or name O or name CB )) or resid 194 through 217 or (resid 218 through 219 an \ d (name N or name CA or name C or name O or name CB )) or resid 220 through 225 \ or (resid 226 and (name N or name CA or name C or name O or name CB )) or resid \ 227 or (resid 228 and (name N or name CA or name C or name O or name CB )) or re \ sid 229 through 276 or (resid 277 through 278 and (name N or name CA or name C o \ r name O or name CB )) or resid 279 through 281 or (resid 282 through 283 and (n \ ame N or name CA or name C or name O or name CB )) or resid 284 or (resid 285 th \ rough 286 and (name N or name CA or name C or name O or name CB )) or resid 288 \ through 291 or (resid 292 and (name N or name CA or name C or name O or name CB \ )) or resid 293 or (resid 294 and (name N or name CA or name C or name O or name \ CB )) or resid 295)) selection = (chain 'd' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 15 or (resid 16 and (name N or name CA \ or name C or name O or name CB )) or resid 17 through 100 or (resid 101 and (na \ me N or name CA or name C or name O or name CB )) or resid 102 through 105 or re \ sid 107 through 113 or (resid 114 and (name N or name CA or name C or name O or \ name CB )) or resid 115 through 123 or (resid 124 and (name N or name CA or name \ C or name O or name CB )) or resid 125 through 128 or (resid 129 and (name N or \ name CA or name C or name O or name CB )) or resid 130 through 149 or resid 151 \ or (resid 152 through 153 and (name N or name CA or name C or name O or name CB \ )) or resid 154 through 161 or (resid 162 and (name N or name CA or name C or n \ ame O or name CB )) or resid 163 through 165 or (resid 166 and (name N or name C \ A or name C or name O or name CB )) or resid 167 through 192 or (resid 193 and ( \ name N or name CA or name C or name O or name CB )) or resid 194 through 217 or \ (resid 218 through 219 and (name N or name CA or name C or name O or name CB )) \ or resid 220 through 225 or (resid 226 and (name N or name CA or name C or name \ O or name CB )) or resid 227 or (resid 228 and (name N or name CA or name C or n \ ame O or name CB )) or resid 229 through 284 or (resid 285 through 286 and (name \ N or name CA or name C or name O or name CB )) or resid 288 through 291 or (res \ id 292 and (name N or name CA or name C or name O or name CB )) or resid 293 or \ (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 295 \ )) selection = (chain 'e' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 15 or (resid 16 and (name N or name CA \ or name C or name O or name CB )) or resid 17 through 75 or resid 83 through 10 \ 0 or (resid 101 and (name N or name CA or name C or name O or name CB )) or resi \ d 102 through 105 or (resid 107 and (name N or name CA or name C or name O or na \ me CB )) or resid 108 through 149 or resid 151 through 161 or (resid 162 and (na \ me N or name CA or name C or name O or name CB )) or resid 163 through 217 or (r \ esid 218 through 219 and (name N or name CA or name C or name O or name CB )) or \ resid 220 through 225 or (resid 226 and (name N or name CA or name C or name O \ or name CB )) or resid 227 through 276 or (resid 277 through 278 and (name N or \ name CA or name C or name O or name CB )) or resid 279 through 281 or (resid 282 \ through 283 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 84 through 285 or (resid 286 and (name N or name CA or name C or name O or name \ CB )) or resid 288 through 293 or (resid 294 and (name N or name CA or name C or \ name O or name CB )) or resid 295)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.24 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: 1.360 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.940 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 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 : 0.006 0.096 10765 Z= 0.409 Angle : 1.309 19.257 14545 Z= 0.712 Chirality : 0.070 0.520 1619 Planarity : 0.008 0.104 1845 Dihedral : 17.744 88.635 3908 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.68 % Favored : 94.09 % Rotamer: Outliers : 0.71 % Allowed : 29.62 % Favored : 69.67 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.20), residues: 1325 helix: -1.89 (0.16), residues: 664 sheet: -0.58 (0.52), residues: 106 loop : -2.27 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.006 TRP E 108 HIS 0.021 0.003 HIS a 36 PHE 0.040 0.004 PHE e 226 TYR 0.050 0.003 TYR e 180 ARG 0.016 0.002 ARG D 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 124 MET cc_start: 0.2874 (mtt) cc_final: 0.2278 (ttp) REVERT: D 245 ILE cc_start: 0.6426 (mm) cc_final: 0.5228 (mm) REVERT: E 61 MET cc_start: 0.3411 (mtm) cc_final: 0.3035 (mtp) REVERT: d 73 TRP cc_start: 0.4312 (m100) cc_final: 0.3274 (m100) REVERT: d 294 MET cc_start: -0.1245 (mtt) cc_final: -0.1748 (mtt) REVERT: e 101 MET cc_start: 0.4668 (mmm) cc_final: 0.2690 (tpt) REVERT: e 279 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7787 (t0) REVERT: A 16 LYS cc_start: 0.8871 (tppt) cc_final: 0.8466 (tppt) REVERT: A 20 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6870 (mp0) outliers start: 8 outliers final: 2 residues processed: 155 average time/residue: 0.2234 time to fit residues: 48.6440 Evaluate side-chains 143 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 279 ASN Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 68 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN E 67 ASN E 206 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 288 ASN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN a 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10765 Z= 0.252 Angle : 0.731 7.190 14545 Z= 0.390 Chirality : 0.046 0.166 1619 Planarity : 0.005 0.108 1845 Dihedral : 6.390 40.523 1463 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.17 % Favored : 95.61 % Rotamer: Outliers : 3.36 % Allowed : 27.94 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.22), residues: 1325 helix: -0.52 (0.19), residues: 675 sheet: -0.46 (0.47), residues: 126 loop : -2.22 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP e 73 HIS 0.009 0.001 HIS D 132 PHE 0.026 0.002 PHE d 72 TYR 0.019 0.002 TYR E 284 ARG 0.009 0.001 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6987 (p90) cc_final: 0.5535 (p90) REVERT: D 141 GLU cc_start: 0.0448 (OUTLIER) cc_final: 0.0097 (mt-10) REVERT: D 204 LEU cc_start: 0.6240 (tp) cc_final: 0.5658 (tt) REVERT: D 207 TYR cc_start: 0.6835 (m-10) cc_final: 0.6493 (m-10) REVERT: E 61 MET cc_start: 0.3855 (mtm) cc_final: 0.3181 (mpp) REVERT: E 81 MET cc_start: 0.8510 (tmm) cc_final: 0.8308 (tmm) REVERT: d 124 MET cc_start: 0.1891 (ptp) cc_final: 0.1502 (ptt) REVERT: d 141 GLU cc_start: 0.3298 (OUTLIER) cc_final: 0.2785 (pp20) REVERT: d 294 MET cc_start: -0.1630 (OUTLIER) cc_final: -0.1845 (mtp) REVERT: A 24 TYR cc_start: 0.7409 (m-80) cc_final: 0.7026 (m-80) REVERT: a 4 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.4509 (ttp80) outliers start: 38 outliers final: 15 residues processed: 169 average time/residue: 0.2172 time to fit residues: 52.5910 Evaluate side-chains 144 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain d residue 50 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 141 GLU Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain d residue 294 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 67 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN ** d 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN A 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5593 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10765 Z= 0.192 Angle : 0.675 10.035 14545 Z= 0.357 Chirality : 0.045 0.158 1619 Planarity : 0.005 0.107 1845 Dihedral : 5.766 24.375 1457 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.23 % Favored : 94.55 % Rotamer: Outliers : 2.21 % Allowed : 27.14 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.22), residues: 1325 helix: 0.06 (0.20), residues: 675 sheet: -0.12 (0.48), residues: 126 loop : -2.24 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 108 HIS 0.014 0.001 HIS d 168 PHE 0.020 0.002 PHE d 72 TYR 0.017 0.002 TYR E 284 ARG 0.006 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6934 (p90) cc_final: 0.5654 (p90) REVERT: D 204 LEU cc_start: 0.6278 (tp) cc_final: 0.5719 (tt) REVERT: D 270 ARG cc_start: 0.6331 (tpm170) cc_final: 0.4944 (tpm170) REVERT: E 132 HIS cc_start: 0.4592 (m-70) cc_final: 0.4225 (t-90) REVERT: d 214 ARG cc_start: 0.3248 (OUTLIER) cc_final: 0.2646 (mmm160) REVERT: d 294 MET cc_start: -0.1806 (OUTLIER) cc_final: -0.2025 (mtp) REVERT: e 101 MET cc_start: 0.5097 (mmm) cc_final: 0.3116 (tpt) REVERT: A 19 ARG cc_start: 0.7547 (mmm160) cc_final: 0.7197 (mmm160) REVERT: A 20 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7221 (mm-30) REVERT: A 24 TYR cc_start: 0.7310 (m-80) cc_final: 0.6978 (m-80) REVERT: a 4 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.4887 (ttp80) outliers start: 25 outliers final: 12 residues processed: 157 average time/residue: 0.2392 time to fit residues: 52.6302 Evaluate side-chains 139 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain d residue 294 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 chunk 13 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 9 GLN ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 192 HIS ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 GLN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 10765 Z= 0.292 Angle : 0.728 8.192 14545 Z= 0.386 Chirality : 0.046 0.238 1619 Planarity : 0.005 0.105 1845 Dihedral : 5.845 25.636 1457 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.45 % Favored : 94.32 % Rotamer: Outliers : 3.18 % Allowed : 26.70 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1325 helix: 0.23 (0.20), residues: 665 sheet: -0.29 (0.47), residues: 123 loop : -2.28 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP d 218 HIS 0.008 0.002 HIS D 89 PHE 0.026 0.002 PHE d 72 TYR 0.018 0.002 TYR E 207 ARG 0.007 0.001 ARG e 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.7134 (p90) cc_final: 0.5761 (p90) REVERT: D 204 LEU cc_start: 0.6244 (tp) cc_final: 0.5848 (tt) REVERT: D 245 ILE cc_start: 0.6304 (mm) cc_final: 0.6024 (mm) REVERT: E 20 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7599 (mtpt) REVERT: E 132 HIS cc_start: 0.4871 (m-70) cc_final: 0.4366 (t-90) REVERT: E 294 MET cc_start: 0.6558 (ptp) cc_final: 0.6348 (ptp) REVERT: d 294 MET cc_start: -0.1652 (OUTLIER) cc_final: -0.1938 (mtp) REVERT: A 19 ARG cc_start: 0.7563 (mmm160) cc_final: 0.7331 (tpt-90) REVERT: A 30 ASN cc_start: 0.6946 (t0) cc_final: 0.6466 (t0) REVERT: a 4 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.4362 (ttp80) REVERT: a 65 LYS cc_start: 0.2313 (OUTLIER) cc_final: 0.1739 (pttt) outliers start: 36 outliers final: 23 residues processed: 163 average time/residue: 0.2280 time to fit residues: 52.7923 Evaluate side-chains 151 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain d residue 45 THR Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain d residue 294 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 78 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN d 58 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 192 HIS ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN A 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5842 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10765 Z= 0.289 Angle : 0.722 8.404 14545 Z= 0.382 Chirality : 0.046 0.236 1619 Planarity : 0.005 0.105 1845 Dihedral : 5.812 24.940 1457 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.29 % Favored : 93.48 % Rotamer: Outliers : 4.24 % Allowed : 25.64 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.22), residues: 1325 helix: 0.20 (0.19), residues: 675 sheet: -0.48 (0.47), residues: 125 loop : -2.30 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 108 HIS 0.017 0.002 HIS e 257 PHE 0.025 0.002 PHE d 72 TYR 0.015 0.002 TYR A 24 ARG 0.006 0.001 ARG d 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 134 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.7094 (p90) cc_final: 0.6750 (p90) REVERT: D 204 LEU cc_start: 0.6096 (tp) cc_final: 0.5839 (tt) REVERT: D 207 TYR cc_start: 0.7047 (m-10) cc_final: 0.6830 (m-10) REVERT: E 132 HIS cc_start: 0.4977 (m-70) cc_final: 0.4487 (t-90) REVERT: E 224 ASN cc_start: 0.6932 (OUTLIER) cc_final: 0.6642 (m-40) REVERT: E 294 MET cc_start: 0.6530 (ptp) cc_final: 0.6274 (ptp) REVERT: d 1 MET cc_start: 0.4621 (pmm) cc_final: 0.3436 (ttt) REVERT: d 45 THR cc_start: 0.8197 (p) cc_final: 0.7995 (p) REVERT: d 124 MET cc_start: 0.2598 (ptp) cc_final: 0.1917 (ptt) REVERT: d 136 PHE cc_start: 0.2319 (OUTLIER) cc_final: 0.2054 (p90) REVERT: d 215 SER cc_start: 0.2734 (OUTLIER) cc_final: 0.1792 (t) REVERT: e 101 MET cc_start: 0.5502 (mmm) cc_final: 0.3499 (tpt) REVERT: A 30 ASN cc_start: 0.6860 (t0) cc_final: 0.6342 (t0) REVERT: a 4 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.4241 (ttp80) REVERT: a 65 LYS cc_start: 0.2396 (OUTLIER) cc_final: 0.1994 (pttt) outliers start: 48 outliers final: 30 residues processed: 168 average time/residue: 0.2200 time to fit residues: 52.3503 Evaluate side-chains 159 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 261 GLN Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 15 ILE Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 HIS Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 78 THR Chi-restraints excluded: chain a residue 81 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN d 92 GLN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 288 ASN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN A 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10765 Z= 0.240 Angle : 0.708 12.614 14545 Z= 0.367 Chirality : 0.046 0.270 1619 Planarity : 0.004 0.104 1845 Dihedral : 5.749 25.308 1457 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.68 % Favored : 94.09 % Rotamer: Outliers : 4.51 % Allowed : 25.46 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.22), residues: 1325 helix: 0.43 (0.19), residues: 662 sheet: -0.49 (0.47), residues: 125 loop : -2.30 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 108 HIS 0.016 0.001 HIS e 257 PHE 0.020 0.002 PHE d 72 TYR 0.016 0.002 TYR d 38 ARG 0.005 0.001 ARG d 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 123 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.7039 (p90) cc_final: 0.6185 (p90) REVERT: D 106 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7870 (ptt90) REVERT: D 204 LEU cc_start: 0.6140 (tp) cc_final: 0.5840 (tt) REVERT: E 132 HIS cc_start: 0.4990 (m-70) cc_final: 0.4538 (t-90) REVERT: E 224 ASN cc_start: 0.6894 (OUTLIER) cc_final: 0.6584 (m110) REVERT: E 294 MET cc_start: 0.6517 (ptp) cc_final: 0.6196 (ptp) REVERT: d 1 MET cc_start: 0.4269 (pmm) cc_final: 0.3203 (ttt) REVERT: d 136 PHE cc_start: 0.2603 (OUTLIER) cc_final: 0.2152 (p90) REVERT: d 215 SER cc_start: 0.2740 (OUTLIER) cc_final: 0.1885 (t) REVERT: e 101 MET cc_start: 0.5532 (mmm) cc_final: 0.3475 (tpt) REVERT: e 250 ILE cc_start: 0.7620 (mt) cc_final: 0.7407 (mm) REVERT: A 16 LYS cc_start: 0.8625 (tppt) cc_final: 0.8362 (tppt) REVERT: a 4 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.4460 (ttp80) REVERT: a 65 LYS cc_start: 0.2460 (OUTLIER) cc_final: 0.2090 (pttt) outliers start: 51 outliers final: 30 residues processed: 163 average time/residue: 0.2233 time to fit residues: 52.0667 Evaluate side-chains 151 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain d residue 28 VAL Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 214 ARG Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 261 GLN Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 15 ILE Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 230 HIS Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS D 134 HIS ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 ASN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 10765 Z= 0.215 Angle : 0.696 12.088 14545 Z= 0.358 Chirality : 0.046 0.277 1619 Planarity : 0.004 0.104 1845 Dihedral : 5.620 24.027 1457 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.36 % Favored : 93.41 % Rotamer: Outliers : 3.45 % Allowed : 26.26 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.94 (0.23), residues: 1325 helix: 0.55 (0.20), residues: 664 sheet: -0.35 (0.48), residues: 125 loop : -2.24 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 108 HIS 0.015 0.002 HIS e 257 PHE 0.019 0.002 PHE E 268 TYR 0.015 0.002 TYR d 184 ARG 0.006 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 123 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.7036 (p90) cc_final: 0.6233 (p90) REVERT: D 204 LEU cc_start: 0.6135 (tp) cc_final: 0.5811 (tt) REVERT: E 63 MET cc_start: 0.6688 (ptp) cc_final: 0.6246 (pmm) REVERT: E 132 HIS cc_start: 0.5128 (m-70) cc_final: 0.4665 (t-90) REVERT: E 224 ASN cc_start: 0.7023 (OUTLIER) cc_final: 0.6657 (m110) REVERT: E 294 MET cc_start: 0.6658 (ptp) cc_final: 0.6450 (ptp) REVERT: d 1 MET cc_start: 0.4671 (pmm) cc_final: 0.3696 (ttt) REVERT: d 136 PHE cc_start: 0.2851 (OUTLIER) cc_final: 0.2031 (p90) REVERT: d 215 SER cc_start: 0.2488 (OUTLIER) cc_final: 0.1925 (t) REVERT: d 252 LEU cc_start: -0.2828 (OUTLIER) cc_final: -0.3130 (tp) REVERT: d 263 MET cc_start: 0.6873 (pmm) cc_final: 0.6072 (pmm) REVERT: e 101 MET cc_start: 0.5699 (mmm) cc_final: 0.3763 (tpt) REVERT: a 4 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.4785 (ttp80) REVERT: a 65 LYS cc_start: 0.2556 (OUTLIER) cc_final: 0.2159 (pttt) outliers start: 39 outliers final: 26 residues processed: 150 average time/residue: 0.2335 time to fit residues: 49.0890 Evaluate side-chains 150 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 224 ASN Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 252 LEU Chi-restraints excluded: chain d residue 261 GLN Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 78 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 79 optimal weight: 0.0870 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 257 HIS e 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10765 Z= 0.235 Angle : 0.710 11.336 14545 Z= 0.366 Chirality : 0.046 0.284 1619 Planarity : 0.004 0.104 1845 Dihedral : 5.580 24.475 1457 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.53 % Favored : 94.24 % Rotamer: Outliers : 3.09 % Allowed : 26.79 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.92 (0.23), residues: 1325 helix: 0.59 (0.20), residues: 667 sheet: -0.37 (0.48), residues: 125 loop : -2.28 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 108 HIS 0.014 0.001 HIS e 257 PHE 0.021 0.002 PHE d 72 TYR 0.015 0.002 TYR E 207 ARG 0.009 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.7002 (p90) cc_final: 0.6287 (p90) REVERT: D 204 LEU cc_start: 0.6119 (tp) cc_final: 0.5811 (tt) REVERT: E 132 HIS cc_start: 0.5130 (m-70) cc_final: 0.4702 (t-90) REVERT: d 1 MET cc_start: 0.4669 (pmm) cc_final: 0.3781 (ttt) REVERT: d 136 PHE cc_start: 0.2981 (OUTLIER) cc_final: 0.1915 (p90) REVERT: d 215 SER cc_start: 0.2334 (OUTLIER) cc_final: 0.1687 (t) REVERT: d 252 LEU cc_start: -0.2691 (OUTLIER) cc_final: -0.3013 (tp) REVERT: d 263 MET cc_start: 0.6802 (pmm) cc_final: 0.5963 (pmm) REVERT: e 101 MET cc_start: 0.5703 (mmm) cc_final: 0.3929 (tpt) REVERT: e 178 LYS cc_start: 0.8977 (pttp) cc_final: 0.8299 (ptmm) REVERT: a 4 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.4552 (ttp80) REVERT: a 65 LYS cc_start: 0.2569 (OUTLIER) cc_final: 0.2164 (pttt) outliers start: 35 outliers final: 28 residues processed: 148 average time/residue: 0.2537 time to fit residues: 52.5562 Evaluate side-chains 153 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 252 LEU Chi-restraints excluded: chain d residue 261 GLN Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 230 HIS Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 57 LYS Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 76 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 120 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 0.0470 chunk 91 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10765 Z= 0.189 Angle : 0.698 9.900 14545 Z= 0.359 Chirality : 0.046 0.286 1619 Planarity : 0.004 0.104 1845 Dihedral : 5.405 23.298 1457 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.68 % Favored : 94.09 % Rotamer: Outliers : 3.18 % Allowed : 27.14 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.78 (0.23), residues: 1325 helix: 0.68 (0.20), residues: 666 sheet: -0.20 (0.49), residues: 126 loop : -2.19 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 108 HIS 0.008 0.001 HIS A 36 PHE 0.017 0.002 PHE E 268 TYR 0.015 0.001 TYR E 207 ARG 0.007 0.001 ARG d 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 2.108 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: D 47 PHE cc_start: 0.6827 (p90) cc_final: 0.6196 (p90) REVERT: D 185 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7039 (tp30) REVERT: D 204 LEU cc_start: 0.5958 (tp) cc_final: 0.5660 (tt) REVERT: E 132 HIS cc_start: 0.5105 (m-70) cc_final: 0.4663 (t-90) REVERT: E 224 ASN cc_start: 0.6976 (p0) cc_final: 0.6725 (m110) REVERT: d 1 MET cc_start: 0.4659 (pmm) cc_final: 0.3813 (ttt) REVERT: d 136 PHE cc_start: 0.2936 (OUTLIER) cc_final: 0.1726 (p90) REVERT: d 215 SER cc_start: 0.2232 (OUTLIER) cc_final: 0.1702 (t) REVERT: d 252 LEU cc_start: -0.2707 (OUTLIER) cc_final: -0.3019 (tp) REVERT: d 263 MET cc_start: 0.6834 (pmm) cc_final: 0.6021 (pmm) REVERT: e 101 MET cc_start: 0.5673 (mmm) cc_final: 0.4055 (tpt) REVERT: e 178 LYS cc_start: 0.8964 (pttp) cc_final: 0.8299 (ptmm) REVERT: a 65 LYS cc_start: 0.2584 (OUTLIER) cc_final: 0.2130 (pttt) outliers start: 36 outliers final: 23 residues processed: 157 average time/residue: 0.2500 time to fit residues: 56.9910 Evaluate side-chains 147 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 252 LEU Chi-restraints excluded: chain d residue 261 GLN Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 158 GLN Chi-restraints excluded: chain e residue 230 HIS Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 57 LYS Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 76 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 129 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 158 GLN e 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 10765 Z= 0.280 Angle : 0.750 10.478 14545 Z= 0.389 Chirality : 0.048 0.308 1619 Planarity : 0.004 0.105 1845 Dihedral : 5.570 25.169 1457 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.68 % Favored : 94.09 % Rotamer: Outliers : 2.39 % Allowed : 27.59 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.94 (0.23), residues: 1325 helix: 0.64 (0.20), residues: 664 sheet: -0.71 (0.45), residues: 144 loop : -2.33 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 108 HIS 0.009 0.001 HIS A 36 PHE 0.024 0.002 PHE d 72 TYR 0.016 0.002 TYR d 210 ARG 0.007 0.001 ARG d 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 PHE cc_start: 0.6938 (p90) cc_final: 0.6478 (p90) REVERT: D 132 HIS cc_start: 0.6189 (m-70) cc_final: 0.5622 (m-70) REVERT: D 204 LEU cc_start: 0.6038 (tp) cc_final: 0.5767 (tt) REVERT: E 132 HIS cc_start: 0.5167 (m-70) cc_final: 0.4682 (t-90) REVERT: d 1 MET cc_start: 0.4679 (pmm) cc_final: 0.3822 (ttt) REVERT: d 136 PHE cc_start: 0.2992 (OUTLIER) cc_final: 0.1702 (p90) REVERT: d 215 SER cc_start: 0.2550 (OUTLIER) cc_final: 0.1944 (t) REVERT: d 263 MET cc_start: 0.6818 (pmm) cc_final: 0.6008 (pmm) REVERT: e 101 MET cc_start: 0.5789 (mmm) cc_final: 0.4143 (tpt) REVERT: e 178 LYS cc_start: 0.8985 (pttp) cc_final: 0.8278 (ptmm) REVERT: a 65 LYS cc_start: 0.2602 (OUTLIER) cc_final: 0.2158 (pttt) outliers start: 27 outliers final: 22 residues processed: 141 average time/residue: 0.2028 time to fit residues: 42.1122 Evaluate side-chains 144 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 257 HIS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 136 PHE Chi-restraints excluded: chain d residue 215 SER Chi-restraints excluded: chain d residue 230 HIS Chi-restraints excluded: chain d residue 261 GLN Chi-restraints excluded: chain d residue 280 ASP Chi-restraints excluded: chain e residue 13 MET Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 158 GLN Chi-restraints excluded: chain e residue 230 HIS Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain a residue 59 VAL Chi-restraints excluded: chain a residue 60 CYS Chi-restraints excluded: chain a residue 65 LYS Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain a residue 81 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.196845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.160719 restraints weight = 69836.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.168548 restraints weight = 33416.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.171488 restraints weight = 16281.107| |-----------------------------------------------------------------------------| r_work (final): 0.4728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4729 r_free = 0.4729 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4729 r_free = 0.4729 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.4729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.225 10765 Z= 0.364 Angle : 0.972 59.200 14545 Z= 0.549 Chirality : 0.051 0.761 1619 Planarity : 0.004 0.104 1845 Dihedral : 5.571 25.129 1457 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.76 % Favored : 94.02 % Rotamer: Outliers : 2.56 % Allowed : 27.41 % Favored : 70.03 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 8.33 % 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: -0.95 (0.23), residues: 1325 helix: 0.63 (0.20), residues: 664 sheet: -0.72 (0.45), residues: 144 loop : -2.33 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 108 HIS 0.008 0.001 HIS A 36 PHE 0.023 0.002 PHE d 72 TYR 0.016 0.002 TYR D 42 ARG 0.007 0.000 ARG d 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2186.75 seconds wall clock time: 40 minutes 35.47 seconds (2435.47 seconds total)