Starting phenix.real_space_refine on Mon Nov 18 10:41:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbk_16543/11_2024/8cbk_16543.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbk_16543/11_2024/8cbk_16543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbk_16543/11_2024/8cbk_16543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbk_16543/11_2024/8cbk_16543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbk_16543/11_2024/8cbk_16543.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbk_16543/11_2024/8cbk_16543.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 1.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 101 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 9874 2.51 5 N 2832 2.21 5 O 3341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16221 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "E" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3814 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 452} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2832 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 9, 'TRANS': 333} Chain: "T" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1971 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 38, 'rna3p_pyr': 37} Link IDs: {'rna2p': 18, 'rna3p': 74} Chain breaks: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9321 SG CYS E 348 62.040 43.374 15.436 1.00196.69 S ATOM 9337 SG CYS E 351 64.801 44.405 12.797 1.00214.65 S ATOM 11179 SG CYS E 578 63.196 47.045 14.911 1.00211.34 S Time building chain proxies: 12.40, per 1000 atoms: 0.76 Number of scatterers: 16221 At special positions: 0 Unit cell: (103.016, 112.144, 166.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 71 16.00 P 101 15.00 Mg 1 11.99 O 3341 8.00 N 2832 7.00 C 9874 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: 5.16 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 557 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 578 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 351 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 348 " Number of angles added : 3 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 11 sheets defined 56.5% alpha, 8.7% beta 33 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.031A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 137 removed outlier: 3.559A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.384A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.839A pdb=" N SER A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.546A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.144A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 122 removed outlier: 3.595A pdb=" N PHE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.792A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 187 removed outlier: 4.362A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.841A pdb=" N THR B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 208' Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.899A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.615A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.333A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.767A pdb=" N SER C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.523A pdb=" N TYR C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 34 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.658A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 122 removed outlier: 3.659A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 186 removed outlier: 4.407A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.615A pdb=" N SER D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.541A pdb=" N TYR D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 129 removed outlier: 3.988A pdb=" N TRP E 124 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'E' and resid 153 through 169 removed outlier: 3.876A pdb=" N VAL E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER E 160 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 188 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 211 through 221 Processing helix chain 'E' and resid 225 through 240 removed outlier: 4.033A pdb=" N VAL E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 278 through 290 removed outlier: 3.679A pdb=" N LEU E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 312 Processing helix chain 'E' and resid 316 through 330 Processing helix chain 'E' and resid 361 through 377 Processing helix chain 'E' and resid 379 through 386 Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 421 through 435 Processing helix chain 'E' and resid 445 through 450 removed outlier: 3.996A pdb=" N ARG E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 467 Processing helix chain 'E' and resid 477 through 490 removed outlier: 4.121A pdb=" N PHE E 481 " --> pdb=" O GLU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 506 Processing helix chain 'E' and resid 510 through 523 Processing helix chain 'F' and resid 62 through 82 Processing helix chain 'F' and resid 89 through 105 removed outlier: 3.863A pdb=" N ALA F 93 " --> pdb=" O ASP F 89 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 Processing helix chain 'F' and resid 125 through 168 removed outlier: 3.865A pdb=" N GLU F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 182 through 202 removed outlier: 3.620A pdb=" N GLN F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 216 through 236 Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 269 removed outlier: 3.565A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 269 " --> pdb=" O TRP F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 283 through 285 No H-bonds generated for 'chain 'F' and resid 283 through 285' Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 374 through 376 No H-bonds generated for 'chain 'F' and resid 374 through 376' Processing helix chain 'F' and resid 388 through 403 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.442A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N ILE A 251 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 195 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.350A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ILE B 251 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B 195 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.398A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 12 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL C 89 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 14 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.455A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 336 through 341 Processing sheet with id=AB1, first strand: chain 'E' and resid 469 through 470 removed outlier: 8.742A pdb=" N PHE E 470 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL E 442 " --> pdb=" O PHE E 470 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL E 407 " --> pdb=" O ILE E 496 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 272 through 273 removed outlier: 8.575A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 5.62 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: 2857 1.33 - 1.45: 4443 1.45 - 1.57: 9092 1.57 - 1.69: 197 1.69 - 1.81: 113 Bond restraints: 16702 Sorted by residual: bond pdb=" O3 NAD A 301 " pdb=" PA NAD A 301 " ideal model delta sigma weight residual 1.653 1.578 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O3 NAD B 301 " pdb=" PA NAD B 301 " ideal model delta sigma weight residual 1.653 1.579 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O3 NAD C 301 " pdb=" PA NAD C 301 " ideal model delta sigma weight residual 1.653 1.581 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" O3 NAD D 301 " pdb=" PA NAD D 301 " ideal model delta sigma weight residual 1.653 1.581 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C2N NAD D 301 " pdb=" C3N NAD D 301 " ideal model delta sigma weight residual 1.381 1.311 0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 16697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 22409 1.41 - 2.81: 480 2.81 - 4.22: 140 4.22 - 5.62: 24 5.62 - 7.03: 10 Bond angle restraints: 23063 Sorted by residual: angle pdb=" N HIS E 447 " pdb=" CA HIS E 447 " pdb=" C HIS E 447 " ideal model delta sigma weight residual 111.07 105.85 5.22 1.07e+00 8.73e-01 2.38e+01 angle pdb=" C GLU E 280 " pdb=" N THR E 281 " pdb=" CA THR E 281 " ideal model delta sigma weight residual 120.65 114.47 6.18 1.32e+00 5.74e-01 2.19e+01 angle pdb=" C TYR F 135 " pdb=" CA TYR F 135 " pdb=" CB TYR F 135 " ideal model delta sigma weight residual 110.90 104.36 6.54 1.58e+00 4.01e-01 1.72e+01 angle pdb=" CA THR F 127 " pdb=" CB THR F 127 " pdb=" OG1 THR F 127 " ideal model delta sigma weight residual 109.60 103.86 5.74 1.50e+00 4.44e-01 1.46e+01 angle pdb=" C PHE E 339 " pdb=" N THR E 340 " pdb=" CA THR E 340 " ideal model delta sigma weight residual 122.82 116.49 6.33 1.68e+00 3.54e-01 1.42e+01 ... (remaining 23058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.50: 9593 26.50 - 52.99: 515 52.99 - 79.49: 150 79.49 - 105.98: 11 105.98 - 132.48: 4 Dihedral angle restraints: 10273 sinusoidal: 5057 harmonic: 5216 Sorted by residual: dihedral pdb=" CA LEU F 385 " pdb=" C LEU F 385 " pdb=" N GLU F 386 " pdb=" CA GLU F 386 " ideal model delta harmonic sigma weight residual 180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" C4' G T 31 " pdb=" C3' G T 31 " pdb=" O3' G T 31 " pdb=" P U T 32 " ideal model delta sinusoidal sigma weight residual -110.00 22.48 -132.48 1 3.50e+01 8.16e-04 1.31e+01 dihedral pdb=" C TYR F 135 " pdb=" N TYR F 135 " pdb=" CA TYR F 135 " pdb=" CB TYR F 135 " ideal model delta harmonic sigma weight residual -122.60 -113.89 -8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 10270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2301 0.047 - 0.094: 274 0.094 - 0.141: 120 0.141 - 0.188: 10 0.188 - 0.235: 3 Chirality restraints: 2708 Sorted by residual: chirality pdb=" CA TYR F 135 " pdb=" N TYR F 135 " pdb=" C TYR F 135 " pdb=" CB TYR F 135 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR E 281 " pdb=" N THR E 281 " pdb=" C THR E 281 " pdb=" CB THR E 281 " both_signs ideal model delta sigma weight residual False 2.53 2.74 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C2' SAH F 501 " pdb=" C1' SAH F 501 " pdb=" C3' SAH F 501 " pdb=" O2' SAH F 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.72 0.19 2.00e-01 2.50e+01 9.04e-01 ... (remaining 2705 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 301 " 0.044 2.00e-02 2.50e+03 2.70e-02 1.45e+01 pdb=" C2N NAD D 301 " -0.035 2.00e-02 2.50e+03 pdb=" C3N NAD D 301 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NAD D 301 " 0.009 2.00e-02 2.50e+03 pdb=" C5N NAD D 301 " 0.005 2.00e-02 2.50e+03 pdb=" C6N NAD D 301 " 0.003 2.00e-02 2.50e+03 pdb=" C7N NAD D 301 " 0.022 2.00e-02 2.50e+03 pdb=" N1N NAD D 301 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 211 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.58e+00 pdb=" C ARG E 211 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG E 211 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY E 212 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 209 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO E 210 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " 0.034 5.00e-02 4.00e+02 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 119 2.51 - 3.10: 12851 3.10 - 3.70: 26962 3.70 - 4.30: 38438 4.30 - 4.90: 61122 Nonbonded interactions: 139492 Sorted by model distance: nonbonded pdb=" OP1 G T 1 " pdb="MG MG T 201 " model vdw 1.908 2.170 nonbonded pdb=" O2' A T 19 " pdb=" OP1 A T 20 " model vdw 2.035 3.040 nonbonded pdb=" OG SER E 361 " pdb=" OE1 GLU E 363 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN F 162 " pdb=" N ILE F 163 " model vdw 2.245 3.120 nonbonded pdb=" O ASP E 510 " pdb=" OG1 THR E 513 " model vdw 2.249 3.040 ... (remaining 139487 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 47.230 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16702 Z= 0.224 Angle : 0.559 7.028 23063 Z= 0.297 Chirality : 0.039 0.235 2708 Planarity : 0.003 0.062 2618 Dihedral : 16.814 132.477 6921 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.21), residues: 1821 helix: 2.53 (0.18), residues: 911 sheet: -0.21 (0.40), residues: 186 loop : -0.28 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 66 HIS 0.008 0.001 HIS F 242 PHE 0.014 0.001 PHE E 288 TYR 0.019 0.001 TYR F 135 ARG 0.003 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8989 (m-30) cc_final: 0.8659 (m-30) REVERT: A 160 GLU cc_start: 0.7944 (pt0) cc_final: 0.7705 (pt0) REVERT: B 48 GLU cc_start: 0.8300 (pm20) cc_final: 0.8068 (pm20) REVERT: B 68 GLU cc_start: 0.8707 (tt0) cc_final: 0.8460 (tt0) REVERT: B 70 ASP cc_start: 0.9200 (m-30) cc_final: 0.8960 (m-30) REVERT: C 211 GLU cc_start: 0.8720 (tp30) cc_final: 0.7975 (tp30) REVERT: D 48 GLU cc_start: 0.8842 (tp30) cc_final: 0.8586 (tp30) REVERT: D 70 ASP cc_start: 0.9080 (m-30) cc_final: 0.8804 (m-30) REVERT: E 148 MET cc_start: 0.8413 (mmp) cc_final: 0.8136 (mmp) REVERT: E 161 LEU cc_start: 0.9632 (mm) cc_final: 0.9391 (mm) REVERT: E 178 LEU cc_start: 0.9194 (tp) cc_final: 0.8925 (tp) REVERT: E 182 LEU cc_start: 0.9791 (mt) cc_final: 0.9577 (mt) REVERT: E 269 GLU cc_start: 0.9175 (tp30) cc_final: 0.8631 (tp30) REVERT: E 283 LYS cc_start: 0.9565 (tmmt) cc_final: 0.9358 (tmmm) REVERT: E 404 PHE cc_start: 0.8009 (m-10) cc_final: 0.7580 (m-10) REVERT: E 455 TRP cc_start: 0.9342 (m100) cc_final: 0.9077 (m100) REVERT: E 505 LYS cc_start: 0.9333 (pptt) cc_final: 0.9083 (pptt) REVERT: E 556 TRP cc_start: 0.8839 (m100) cc_final: 0.8274 (m100) REVERT: F 116 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8811 (mp0) REVERT: F 209 MET cc_start: 0.9014 (mpp) cc_final: 0.8286 (mpt) REVERT: F 314 ASP cc_start: 0.8926 (p0) cc_final: 0.8427 (p0) REVERT: F 371 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8712 (mt-10) outliers start: 2 outliers final: 1 residues processed: 316 average time/residue: 1.2501 time to fit residues: 439.2807 Evaluate side-chains 252 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 447 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.9990 chunk 144 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 152 ASN C 260 GLN E 258 GLN E 273 HIS E 424 GLN E 447 HIS F 147 GLN F 348 ASN F 390 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16702 Z= 0.183 Angle : 0.644 13.727 23063 Z= 0.314 Chirality : 0.042 0.345 2708 Planarity : 0.004 0.063 2618 Dihedral : 16.099 126.036 3561 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.80 % Allowed : 9.99 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 1821 helix: 2.39 (0.17), residues: 916 sheet: -0.23 (0.35), residues: 234 loop : -0.04 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 124 HIS 0.006 0.001 HIS F 242 PHE 0.021 0.001 PHE E 481 TYR 0.013 0.001 TYR E 365 ARG 0.004 0.000 ARG E 515 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 304 time to evaluate : 1.690 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: A 70 ASP cc_start: 0.8901 (m-30) cc_final: 0.8551 (m-30) REVERT: A 119 ASP cc_start: 0.9012 (m-30) cc_final: 0.8756 (m-30) REVERT: B 64 ASP cc_start: 0.8465 (t0) cc_final: 0.8234 (t0) REVERT: B 68 GLU cc_start: 0.8612 (tt0) cc_final: 0.8386 (tt0) REVERT: B 70 ASP cc_start: 0.9132 (m-30) cc_final: 0.8807 (m-30) REVERT: B 160 GLU cc_start: 0.8802 (mp0) cc_final: 0.8325 (pm20) REVERT: C 70 ASP cc_start: 0.9149 (m-30) cc_final: 0.8948 (m-30) REVERT: C 211 GLU cc_start: 0.8531 (tp30) cc_final: 0.7796 (tp30) REVERT: D 48 GLU cc_start: 0.8711 (tp30) cc_final: 0.8327 (tp30) REVERT: D 70 ASP cc_start: 0.9025 (m-30) cc_final: 0.8738 (m-30) REVERT: E 148 MET cc_start: 0.8265 (mmp) cc_final: 0.7925 (mmp) REVERT: E 161 LEU cc_start: 0.9649 (mm) cc_final: 0.9445 (mm) REVERT: E 182 LEU cc_start: 0.9740 (mt) cc_final: 0.9527 (mt) REVERT: E 209 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8283 (tp30) REVERT: E 248 ASN cc_start: 0.9482 (t0) cc_final: 0.9198 (OUTLIER) REVERT: E 266 LEU cc_start: 0.9383 (tm) cc_final: 0.9025 (tm) REVERT: E 283 LYS cc_start: 0.9512 (tmmt) cc_final: 0.9288 (tmmm) REVERT: E 285 PHE cc_start: 0.8647 (t80) cc_final: 0.7815 (t80) REVERT: E 288 PHE cc_start: 0.8416 (t80) cc_final: 0.8002 (t80) REVERT: E 291 ASP cc_start: 0.8339 (p0) cc_final: 0.8136 (p0) REVERT: E 312 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8685 (tm-30) REVERT: E 326 TRP cc_start: 0.9432 (t-100) cc_final: 0.9167 (t-100) REVERT: E 353 LYS cc_start: 0.9201 (mmpt) cc_final: 0.8789 (mttt) REVERT: E 404 PHE cc_start: 0.7921 (m-80) cc_final: 0.7583 (m-10) REVERT: E 427 LEU cc_start: 0.9298 (pp) cc_final: 0.9064 (pp) REVERT: E 448 MET cc_start: 0.9447 (tmm) cc_final: 0.8903 (tpt) REVERT: E 455 TRP cc_start: 0.9252 (m100) cc_final: 0.7917 (m100) REVERT: E 526 LEU cc_start: 0.8882 (mm) cc_final: 0.8149 (mm) REVERT: F 100 MET cc_start: 0.9412 (mmm) cc_final: 0.8271 (mmm) REVERT: F 101 TRP cc_start: 0.9445 (m100) cc_final: 0.9131 (m100) REVERT: F 116 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8774 (mp0) REVERT: F 184 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8692 (t70) REVERT: F 314 ASP cc_start: 0.8977 (p0) cc_final: 0.8690 (p0) REVERT: F 345 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8187 (tm-30) REVERT: F 371 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8721 (mt-10) outliers start: 12 outliers final: 6 residues processed: 306 average time/residue: 1.2551 time to fit residues: 428.0898 Evaluate side-chains 245 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 239 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 171 optimal weight: 0.0980 chunk 58 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN E 396 ASN E 514 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16702 Z= 0.238 Angle : 0.623 10.351 23063 Z= 0.309 Chirality : 0.042 0.288 2708 Planarity : 0.004 0.062 2618 Dihedral : 16.034 126.878 3559 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.73 % Allowed : 13.25 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.63 (0.20), residues: 1821 helix: 2.29 (0.17), residues: 910 sheet: -0.24 (0.34), residues: 234 loop : -0.04 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP F 66 HIS 0.009 0.001 HIS F 242 PHE 0.028 0.001 PHE E 518 TYR 0.014 0.001 TYR E 267 ARG 0.003 0.000 ARG E 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.9009 (m-30) cc_final: 0.8682 (m-30) REVERT: B 64 ASP cc_start: 0.8506 (t0) cc_final: 0.8279 (t0) REVERT: B 68 GLU cc_start: 0.8638 (tt0) cc_final: 0.8429 (tt0) REVERT: B 70 ASP cc_start: 0.9189 (m-30) cc_final: 0.8869 (m-30) REVERT: B 118 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9266 (mp) REVERT: B 160 GLU cc_start: 0.8856 (mp0) cc_final: 0.8393 (pm20) REVERT: C 70 ASP cc_start: 0.9153 (m-30) cc_final: 0.8894 (m-30) REVERT: C 211 GLU cc_start: 0.8527 (tp30) cc_final: 0.7770 (tp30) REVERT: D 48 GLU cc_start: 0.8716 (tp30) cc_final: 0.8342 (tp30) REVERT: D 70 ASP cc_start: 0.9061 (m-30) cc_final: 0.8777 (m-30) REVERT: D 86 ASP cc_start: 0.9134 (m-30) cc_final: 0.8882 (m-30) REVERT: E 148 MET cc_start: 0.8244 (mmp) cc_final: 0.7930 (mmp) REVERT: E 234 GLU cc_start: 0.9220 (tp30) cc_final: 0.8784 (tp30) REVERT: E 266 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8969 (tm) REVERT: E 283 LYS cc_start: 0.9445 (tmmt) cc_final: 0.9130 (tmmm) REVERT: E 288 PHE cc_start: 0.8609 (t80) cc_final: 0.8142 (t80) REVERT: E 353 LYS cc_start: 0.9225 (mmpt) cc_final: 0.8882 (mttt) REVERT: E 404 PHE cc_start: 0.7945 (m-80) cc_final: 0.7567 (m-10) REVERT: E 426 LEU cc_start: 0.9732 (tt) cc_final: 0.9471 (pp) REVERT: E 518 PHE cc_start: 0.9457 (t80) cc_final: 0.9241 (t80) REVERT: E 556 TRP cc_start: 0.9048 (m-90) cc_final: 0.8798 (m-90) REVERT: F 95 ARG cc_start: 0.8934 (mmt180) cc_final: 0.8731 (mtt180) REVERT: F 116 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8823 (mp0) REVERT: F 257 GLU cc_start: 0.8932 (tp30) cc_final: 0.8564 (mm-30) REVERT: F 314 ASP cc_start: 0.9041 (p0) cc_final: 0.8672 (p0) REVERT: F 345 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8273 (tm-30) REVERT: F 371 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8764 (mt-10) outliers start: 26 outliers final: 10 residues processed: 267 average time/residue: 1.2635 time to fit residues: 375.6754 Evaluate side-chains 234 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 222 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 486 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN C 260 GLN E 454 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16702 Z= 0.191 Angle : 0.626 13.444 23063 Z= 0.307 Chirality : 0.041 0.287 2708 Planarity : 0.004 0.060 2618 Dihedral : 15.931 126.822 3559 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.93 % Allowed : 14.71 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.65 (0.20), residues: 1821 helix: 2.30 (0.17), residues: 911 sheet: -0.19 (0.33), residues: 239 loop : -0.04 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP E 226 HIS 0.008 0.001 HIS E 152 PHE 0.028 0.001 PHE E 481 TYR 0.023 0.001 TYR E 484 ARG 0.004 0.000 ARG E 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 1.687 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: A 70 ASP cc_start: 0.8833 (m-30) cc_final: 0.8537 (m-30) REVERT: A 119 ASP cc_start: 0.8969 (m-30) cc_final: 0.8758 (m-30) REVERT: B 64 ASP cc_start: 0.8428 (t0) cc_final: 0.8207 (t0) REVERT: B 68 GLU cc_start: 0.8626 (tt0) cc_final: 0.8351 (tt0) REVERT: B 70 ASP cc_start: 0.9172 (m-30) cc_final: 0.8845 (m-30) REVERT: B 118 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9261 (mp) REVERT: B 160 GLU cc_start: 0.8841 (mp0) cc_final: 0.8398 (pm20) REVERT: C 70 ASP cc_start: 0.9153 (m-30) cc_final: 0.8856 (m-30) REVERT: C 211 GLU cc_start: 0.8484 (tp30) cc_final: 0.7694 (tp30) REVERT: D 70 ASP cc_start: 0.9053 (m-30) cc_final: 0.8761 (m-30) REVERT: D 86 ASP cc_start: 0.9129 (m-30) cc_final: 0.8859 (m-30) REVERT: E 148 MET cc_start: 0.8255 (mmp) cc_final: 0.7956 (mmp) REVERT: E 283 LYS cc_start: 0.9412 (tmmt) cc_final: 0.9105 (tmmm) REVERT: E 288 PHE cc_start: 0.8602 (t80) cc_final: 0.8195 (t80) REVERT: E 353 LYS cc_start: 0.9224 (mmpt) cc_final: 0.8872 (mttt) REVERT: E 404 PHE cc_start: 0.7929 (m-80) cc_final: 0.7540 (m-10) REVERT: E 426 LEU cc_start: 0.9713 (tt) cc_final: 0.9443 (pp) REVERT: E 427 LEU cc_start: 0.9367 (pp) cc_final: 0.9014 (pp) REVERT: E 521 GLN cc_start: 0.9506 (tm-30) cc_final: 0.8899 (tm-30) REVERT: F 95 ARG cc_start: 0.8859 (mmt180) cc_final: 0.8499 (mtt180) REVERT: F 257 GLU cc_start: 0.8893 (tp30) cc_final: 0.8527 (mm-30) REVERT: F 314 ASP cc_start: 0.9050 (p0) cc_final: 0.8610 (p0) REVERT: F 345 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8193 (tm-30) REVERT: F 371 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8756 (mt-10) outliers start: 29 outliers final: 12 residues processed: 251 average time/residue: 1.2779 time to fit residues: 360.4495 Evaluate side-chains 234 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 221 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN C 260 GLN E 540 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16702 Z= 0.309 Angle : 0.667 18.328 23063 Z= 0.325 Chirality : 0.043 0.311 2708 Planarity : 0.004 0.057 2618 Dihedral : 15.936 128.813 3559 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.06 % Allowed : 16.05 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.52 (0.20), residues: 1821 helix: 2.17 (0.17), residues: 909 sheet: -0.17 (0.33), residues: 225 loop : -0.09 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP F 66 HIS 0.007 0.001 HIS E 152 PHE 0.019 0.001 PHE F 97 TYR 0.018 0.001 TYR E 314 ARG 0.003 0.000 ARG E 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 1.757 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: A 70 ASP cc_start: 0.8857 (m-30) cc_final: 0.8554 (m-30) REVERT: A 119 ASP cc_start: 0.8993 (m-30) cc_final: 0.8610 (m-30) REVERT: B 64 ASP cc_start: 0.8514 (t0) cc_final: 0.8298 (t0) REVERT: B 68 GLU cc_start: 0.8648 (tt0) cc_final: 0.8369 (tt0) REVERT: B 70 ASP cc_start: 0.9208 (m-30) cc_final: 0.8887 (m-30) REVERT: B 118 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9258 (mp) REVERT: B 135 GLU cc_start: 0.8849 (mp0) cc_final: 0.8628 (mp0) REVERT: B 160 GLU cc_start: 0.8890 (mp0) cc_final: 0.8421 (pm20) REVERT: C 70 ASP cc_start: 0.9184 (m-30) cc_final: 0.8904 (m-30) REVERT: C 211 GLU cc_start: 0.8493 (tp30) cc_final: 0.7723 (tp30) REVERT: D 70 ASP cc_start: 0.9098 (m-30) cc_final: 0.8795 (m-30) REVERT: D 86 ASP cc_start: 0.9146 (m-30) cc_final: 0.8880 (m-30) REVERT: D 135 GLU cc_start: 0.9030 (tp30) cc_final: 0.8747 (mm-30) REVERT: E 148 MET cc_start: 0.8393 (mmp) cc_final: 0.8102 (mmp) REVERT: E 269 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8988 (pm20) REVERT: E 283 LYS cc_start: 0.9420 (tmmt) cc_final: 0.9115 (tmmm) REVERT: E 288 PHE cc_start: 0.8642 (t80) cc_final: 0.8096 (t80) REVERT: E 307 TYR cc_start: 0.9238 (t80) cc_final: 0.8856 (t80) REVERT: E 353 LYS cc_start: 0.9272 (mmpt) cc_final: 0.8922 (mttt) REVERT: E 404 PHE cc_start: 0.7953 (m-80) cc_final: 0.7613 (m-10) REVERT: E 426 LEU cc_start: 0.9714 (tt) cc_final: 0.9477 (pp) REVERT: E 427 LEU cc_start: 0.9364 (pp) cc_final: 0.9026 (pp) REVERT: E 448 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8831 (tpt) REVERT: E 521 GLN cc_start: 0.9528 (tm-30) cc_final: 0.9226 (tm-30) REVERT: E 556 TRP cc_start: 0.9041 (m-90) cc_final: 0.8807 (m-90) REVERT: F 95 ARG cc_start: 0.8926 (mtt180) cc_final: 0.8703 (mmt180) REVERT: F 107 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8507 (mm-30) REVERT: F 257 GLU cc_start: 0.8967 (tp30) cc_final: 0.8600 (mm-30) REVERT: F 314 ASP cc_start: 0.9036 (p0) cc_final: 0.8679 (p0) REVERT: F 345 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8224 (tm-30) REVERT: F 371 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8769 (mt-10) outliers start: 31 outliers final: 13 residues processed: 251 average time/residue: 1.2941 time to fit residues: 360.4358 Evaluate side-chains 228 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 448 MET Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16702 Z= 0.215 Angle : 0.661 18.858 23063 Z= 0.321 Chirality : 0.041 0.289 2708 Planarity : 0.004 0.056 2618 Dihedral : 15.877 128.482 3559 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.26 % Allowed : 16.91 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.45 (0.20), residues: 1821 helix: 2.07 (0.17), residues: 918 sheet: -0.11 (0.33), residues: 223 loop : -0.15 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP F 66 HIS 0.009 0.001 HIS E 152 PHE 0.026 0.001 PHE E 481 TYR 0.014 0.001 TYR E 484 ARG 0.003 0.000 ARG F 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 1.733 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: A 70 ASP cc_start: 0.8840 (m-30) cc_final: 0.8518 (m-30) REVERT: A 119 ASP cc_start: 0.8993 (m-30) cc_final: 0.8741 (m-30) REVERT: A 142 ASP cc_start: 0.8901 (t0) cc_final: 0.8696 (t0) REVERT: B 64 ASP cc_start: 0.8415 (t0) cc_final: 0.8210 (t0) REVERT: B 68 GLU cc_start: 0.8628 (tt0) cc_final: 0.8370 (tt0) REVERT: B 70 ASP cc_start: 0.9182 (m-30) cc_final: 0.8855 (m-30) REVERT: B 118 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9255 (mp) REVERT: B 143 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8876 (mp-120) REVERT: B 160 GLU cc_start: 0.8863 (mp0) cc_final: 0.8414 (pm20) REVERT: C 70 ASP cc_start: 0.9179 (m-30) cc_final: 0.8874 (m-30) REVERT: C 86 ASP cc_start: 0.9083 (m-30) cc_final: 0.8839 (m-30) REVERT: C 211 GLU cc_start: 0.8476 (tp30) cc_final: 0.7695 (tp30) REVERT: D 70 ASP cc_start: 0.9084 (m-30) cc_final: 0.8799 (m-30) REVERT: D 86 ASP cc_start: 0.9134 (m-30) cc_final: 0.8866 (m-30) REVERT: D 135 GLU cc_start: 0.9033 (tp30) cc_final: 0.8805 (mm-30) REVERT: E 120 ASN cc_start: 0.8896 (p0) cc_final: 0.8134 (p0) REVERT: E 122 GLU cc_start: 0.8958 (tp30) cc_final: 0.8660 (pp20) REVERT: E 148 MET cc_start: 0.8220 (mmp) cc_final: 0.7980 (mmp) REVERT: E 266 LEU cc_start: 0.9356 (tm) cc_final: 0.9059 (tm) REVERT: E 269 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8990 (pm20) REVERT: E 283 LYS cc_start: 0.9397 (tmmt) cc_final: 0.9078 (tmmm) REVERT: E 288 PHE cc_start: 0.8614 (t80) cc_final: 0.8156 (t80) REVERT: E 307 TYR cc_start: 0.9184 (t80) cc_final: 0.8783 (t80) REVERT: E 353 LYS cc_start: 0.9257 (mmpt) cc_final: 0.8918 (mttt) REVERT: E 404 PHE cc_start: 0.7894 (m-80) cc_final: 0.7563 (m-10) REVERT: E 426 LEU cc_start: 0.9708 (tt) cc_final: 0.9482 (pp) REVERT: E 427 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9017 (pp) REVERT: E 446 LYS cc_start: 0.9673 (mttt) cc_final: 0.9424 (mmmt) REVERT: E 448 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8791 (tpt) REVERT: E 473 ASP cc_start: 0.8982 (p0) cc_final: 0.8635 (p0) REVERT: E 521 GLN cc_start: 0.9526 (tm-30) cc_final: 0.9223 (tm-30) REVERT: F 254 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9402 (tt) REVERT: F 257 GLU cc_start: 0.8940 (tp30) cc_final: 0.8572 (mm-30) REVERT: F 314 ASP cc_start: 0.9044 (p0) cc_final: 0.8664 (p0) REVERT: F 345 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8241 (tm-30) REVERT: F 371 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8764 (mt-10) outliers start: 34 outliers final: 16 residues processed: 256 average time/residue: 1.2765 time to fit residues: 363.5011 Evaluate side-chains 238 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 448 MET Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN E 310 ASN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16702 Z= 0.226 Angle : 0.664 17.054 23063 Z= 0.326 Chirality : 0.041 0.313 2708 Planarity : 0.004 0.057 2618 Dihedral : 15.837 128.707 3559 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.20 % Allowed : 18.31 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.40 (0.20), residues: 1821 helix: 2.05 (0.17), residues: 916 sheet: -0.08 (0.33), residues: 223 loop : -0.20 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP F 66 HIS 0.008 0.001 HIS E 152 PHE 0.015 0.001 PHE F 97 TYR 0.021 0.001 TYR E 213 ARG 0.006 0.000 ARG F 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8867 (m-30) cc_final: 0.8556 (m-30) REVERT: A 119 ASP cc_start: 0.8994 (m-30) cc_final: 0.8725 (m-30) REVERT: B 41 ASP cc_start: 0.9126 (t0) cc_final: 0.8917 (t70) REVERT: B 68 GLU cc_start: 0.8632 (tt0) cc_final: 0.8350 (tt0) REVERT: B 70 ASP cc_start: 0.9194 (m-30) cc_final: 0.8868 (m-30) REVERT: B 118 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9249 (mp) REVERT: B 160 GLU cc_start: 0.8873 (mp0) cc_final: 0.8410 (pm20) REVERT: C 70 ASP cc_start: 0.9178 (m-30) cc_final: 0.8863 (m-30) REVERT: C 86 ASP cc_start: 0.9095 (m-30) cc_final: 0.8871 (m-30) REVERT: C 211 GLU cc_start: 0.8482 (tp30) cc_final: 0.7701 (tp30) REVERT: D 70 ASP cc_start: 0.9085 (m-30) cc_final: 0.8801 (m-30) REVERT: D 86 ASP cc_start: 0.9148 (m-30) cc_final: 0.8889 (m-30) REVERT: D 135 GLU cc_start: 0.9015 (tp30) cc_final: 0.8763 (mm-30) REVERT: E 120 ASN cc_start: 0.8959 (p0) cc_final: 0.8156 (p0) REVERT: E 122 GLU cc_start: 0.8991 (tp30) cc_final: 0.8654 (pp20) REVERT: E 148 MET cc_start: 0.8123 (mmp) cc_final: 0.7901 (mmp) REVERT: E 234 GLU cc_start: 0.9151 (tp30) cc_final: 0.8590 (tp30) REVERT: E 266 LEU cc_start: 0.9356 (tm) cc_final: 0.9119 (tm) REVERT: E 269 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8985 (pm20) REVERT: E 283 LYS cc_start: 0.9401 (tmmt) cc_final: 0.9089 (tmmm) REVERT: E 288 PHE cc_start: 0.8592 (t80) cc_final: 0.8065 (t80) REVERT: E 353 LYS cc_start: 0.9269 (mmpt) cc_final: 0.8963 (mttt) REVERT: E 404 PHE cc_start: 0.7914 (m-80) cc_final: 0.7568 (m-10) REVERT: E 426 LEU cc_start: 0.9706 (tt) cc_final: 0.9480 (pp) REVERT: E 427 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9004 (pp) REVERT: E 448 MET cc_start: 0.9254 (tpt) cc_final: 0.8804 (tpt) REVERT: E 473 ASP cc_start: 0.8964 (p0) cc_final: 0.8646 (p0) REVERT: E 514 GLN cc_start: 0.9386 (tt0) cc_final: 0.9156 (mt0) REVERT: E 521 GLN cc_start: 0.9514 (tm-30) cc_final: 0.9216 (tm-30) REVERT: F 63 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9102 (pt) REVERT: F 95 ARG cc_start: 0.8875 (mmt180) cc_final: 0.8586 (mmt180) REVERT: F 107 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8344 (mm-30) REVERT: F 254 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9400 (tt) REVERT: F 257 GLU cc_start: 0.8955 (tp30) cc_final: 0.8582 (mm-30) REVERT: F 314 ASP cc_start: 0.9038 (p0) cc_final: 0.8650 (p0) REVERT: F 345 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8255 (tm-30) REVERT: F 371 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8774 (mt-10) outliers start: 33 outliers final: 17 residues processed: 239 average time/residue: 1.2406 time to fit residues: 331.4729 Evaluate side-chains 238 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.3980 chunk 109 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN C 260 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16702 Z= 0.181 Angle : 0.676 16.647 23063 Z= 0.332 Chirality : 0.042 0.334 2708 Planarity : 0.004 0.057 2618 Dihedral : 15.752 127.660 3559 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.00 % Allowed : 18.91 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.35 (0.20), residues: 1821 helix: 2.01 (0.17), residues: 922 sheet: 0.00 (0.33), residues: 231 loop : -0.30 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP F 66 HIS 0.009 0.001 HIS E 152 PHE 0.024 0.001 PHE E 481 TYR 0.013 0.001 TYR E 307 ARG 0.006 0.000 ARG F 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 1.776 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: A 70 ASP cc_start: 0.8850 (m-30) cc_final: 0.8538 (m-30) REVERT: A 119 ASP cc_start: 0.8976 (m-30) cc_final: 0.8750 (m-30) REVERT: B 41 ASP cc_start: 0.9106 (t0) cc_final: 0.8836 (t70) REVERT: B 68 GLU cc_start: 0.8629 (tt0) cc_final: 0.8362 (tt0) REVERT: B 70 ASP cc_start: 0.9198 (m-30) cc_final: 0.8875 (m-30) REVERT: B 160 GLU cc_start: 0.8844 (mp0) cc_final: 0.8387 (pm20) REVERT: B 259 MET cc_start: 0.9412 (mmm) cc_final: 0.9114 (mmm) REVERT: B 260 GLN cc_start: 0.9149 (mm110) cc_final: 0.6659 (pt0) REVERT: C 70 ASP cc_start: 0.9158 (m-30) cc_final: 0.8844 (m-30) REVERT: C 86 ASP cc_start: 0.9089 (m-30) cc_final: 0.8857 (m-30) REVERT: C 211 GLU cc_start: 0.8427 (tp30) cc_final: 0.7805 (tp30) REVERT: C 249 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: D 70 ASP cc_start: 0.9081 (m-30) cc_final: 0.8803 (m-30) REVERT: D 86 ASP cc_start: 0.9130 (m-30) cc_final: 0.8848 (m-30) REVERT: D 135 GLU cc_start: 0.9003 (tp30) cc_final: 0.8796 (mm-30) REVERT: E 120 ASN cc_start: 0.8918 (p0) cc_final: 0.7994 (p0) REVERT: E 122 GLU cc_start: 0.8989 (tp30) cc_final: 0.8649 (pp20) REVERT: E 234 GLU cc_start: 0.9112 (tp30) cc_final: 0.8528 (tp30) REVERT: E 266 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8908 (tm) REVERT: E 283 LYS cc_start: 0.9391 (tmmt) cc_final: 0.9077 (tmmm) REVERT: E 288 PHE cc_start: 0.8557 (t80) cc_final: 0.8047 (t80) REVERT: E 353 LYS cc_start: 0.9255 (mmpt) cc_final: 0.8964 (mttt) REVERT: E 404 PHE cc_start: 0.7830 (m-80) cc_final: 0.7480 (m-10) REVERT: E 426 LEU cc_start: 0.9699 (tt) cc_final: 0.9466 (pp) REVERT: E 427 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8997 (pp) REVERT: E 448 MET cc_start: 0.9293 (tpt) cc_final: 0.8857 (tpt) REVERT: E 514 GLN cc_start: 0.9364 (tt0) cc_final: 0.9151 (mt0) REVERT: E 521 GLN cc_start: 0.9491 (tm-30) cc_final: 0.9251 (tm-30) REVERT: E 556 TRP cc_start: 0.8869 (m-90) cc_final: 0.8646 (m-90) REVERT: E 564 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9115 (mm) REVERT: F 95 ARG cc_start: 0.8824 (mmt180) cc_final: 0.8513 (mmt180) REVERT: F 107 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8278 (tp30) REVERT: F 254 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9405 (tt) REVERT: F 257 GLU cc_start: 0.8928 (tp30) cc_final: 0.8553 (mm-30) REVERT: F 314 ASP cc_start: 0.9037 (p0) cc_final: 0.8622 (p0) REVERT: F 345 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8273 (tm-30) REVERT: F 371 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8749 (mt-10) outliers start: 30 outliers final: 16 residues processed: 241 average time/residue: 1.1743 time to fit residues: 316.7489 Evaluate side-chains 237 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.7980 chunk 170 optimal weight: 0.0980 chunk 175 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 0.0030 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN D 152 ASN E 265 ASN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16702 Z= 0.207 Angle : 0.685 16.060 23063 Z= 0.335 Chirality : 0.043 0.415 2708 Planarity : 0.004 0.058 2618 Dihedral : 15.715 127.749 3559 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.66 % Allowed : 19.37 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.31 (0.20), residues: 1821 helix: 1.97 (0.17), residues: 924 sheet: 0.01 (0.33), residues: 231 loop : -0.33 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP F 66 HIS 0.008 0.001 HIS E 152 PHE 0.011 0.001 PHE E 481 TYR 0.023 0.001 TYR F 135 ARG 0.006 0.000 ARG F 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8855 (m-30) cc_final: 0.8540 (m-30) REVERT: A 119 ASP cc_start: 0.8972 (m-30) cc_final: 0.8707 (m-30) REVERT: B 70 ASP cc_start: 0.9218 (m-30) cc_final: 0.8892 (m-30) REVERT: B 135 GLU cc_start: 0.8871 (mp0) cc_final: 0.8658 (mp0) REVERT: B 160 GLU cc_start: 0.8853 (mp0) cc_final: 0.8390 (pm20) REVERT: B 232 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8745 (mt-10) REVERT: B 260 GLN cc_start: 0.9153 (mm110) cc_final: 0.6636 (pt0) REVERT: C 70 ASP cc_start: 0.9165 (m-30) cc_final: 0.8864 (m-30) REVERT: C 86 ASP cc_start: 0.9102 (m-30) cc_final: 0.8895 (m-30) REVERT: C 211 GLU cc_start: 0.8444 (tp30) cc_final: 0.7659 (tp30) REVERT: C 249 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: D 70 ASP cc_start: 0.9091 (m-30) cc_final: 0.8802 (m-30) REVERT: D 86 ASP cc_start: 0.9148 (m-30) cc_final: 0.8874 (m-30) REVERT: D 135 GLU cc_start: 0.9014 (tp30) cc_final: 0.8769 (mm-30) REVERT: E 120 ASN cc_start: 0.8950 (p0) cc_final: 0.8083 (p0) REVERT: E 122 GLU cc_start: 0.8983 (tp30) cc_final: 0.8639 (pp20) REVERT: E 148 MET cc_start: 0.8094 (mmp) cc_final: 0.7864 (mmp) REVERT: E 234 GLU cc_start: 0.9101 (tp30) cc_final: 0.8497 (tp30) REVERT: E 283 LYS cc_start: 0.9410 (tmmt) cc_final: 0.9094 (tmmm) REVERT: E 288 PHE cc_start: 0.8572 (t80) cc_final: 0.8041 (t80) REVERT: E 353 LYS cc_start: 0.9260 (mmpt) cc_final: 0.8976 (mttt) REVERT: E 404 PHE cc_start: 0.7858 (m-80) cc_final: 0.7522 (m-10) REVERT: E 415 LYS cc_start: 0.8793 (ptmt) cc_final: 0.8438 (ptpp) REVERT: E 426 LEU cc_start: 0.9694 (tt) cc_final: 0.9465 (pp) REVERT: E 427 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8988 (pp) REVERT: E 448 MET cc_start: 0.9310 (tpt) cc_final: 0.8907 (tpt) REVERT: E 521 GLN cc_start: 0.9482 (tm-30) cc_final: 0.9173 (tm-30) REVERT: E 556 TRP cc_start: 0.8907 (m-90) cc_final: 0.8706 (m-90) REVERT: E 564 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9116 (mm) REVERT: F 95 ARG cc_start: 0.8845 (mmt180) cc_final: 0.8523 (mmt180) REVERT: F 107 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8325 (mm-30) REVERT: F 254 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9416 (tt) REVERT: F 257 GLU cc_start: 0.8947 (tp30) cc_final: 0.8572 (mm-30) REVERT: F 314 ASP cc_start: 0.9040 (p0) cc_final: 0.8609 (p0) REVERT: F 345 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8286 (tm-30) REVERT: F 371 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8769 (mt-10) outliers start: 25 outliers final: 14 residues processed: 236 average time/residue: 1.1922 time to fit residues: 314.8068 Evaluate side-chains 233 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 189 optimal weight: 40.0000 chunk 174 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16702 Z= 0.203 Angle : 0.714 16.326 23063 Z= 0.347 Chirality : 0.045 0.542 2708 Planarity : 0.004 0.058 2618 Dihedral : 15.687 127.539 3559 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.40 % Allowed : 20.11 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.26 (0.20), residues: 1821 helix: 1.93 (0.17), residues: 924 sheet: -0.01 (0.33), residues: 231 loop : -0.34 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP F 66 HIS 0.009 0.001 HIS E 152 PHE 0.022 0.001 PHE E 481 TYR 0.034 0.002 TYR E 307 ARG 0.013 0.000 ARG F 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 1.481 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: A 70 ASP cc_start: 0.8863 (m-30) cc_final: 0.8538 (m-30) REVERT: A 119 ASP cc_start: 0.8953 (m-30) cc_final: 0.8734 (m-30) REVERT: A 142 ASP cc_start: 0.8857 (t0) cc_final: 0.8525 (t0) REVERT: B 41 ASP cc_start: 0.9133 (t0) cc_final: 0.8931 (t0) REVERT: B 70 ASP cc_start: 0.9225 (m-30) cc_final: 0.8905 (m-30) REVERT: B 135 GLU cc_start: 0.8895 (mp0) cc_final: 0.8681 (mp0) REVERT: B 160 GLU cc_start: 0.8846 (mp0) cc_final: 0.8378 (pm20) REVERT: B 260 GLN cc_start: 0.9106 (mm110) cc_final: 0.6709 (pt0) REVERT: C 70 ASP cc_start: 0.9167 (m-30) cc_final: 0.8856 (m-30) REVERT: C 86 ASP cc_start: 0.9114 (m-30) cc_final: 0.8832 (m-30) REVERT: C 211 GLU cc_start: 0.8425 (tp30) cc_final: 0.7713 (tp30) REVERT: C 249 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: D 70 ASP cc_start: 0.9079 (m-30) cc_final: 0.8796 (m-30) REVERT: D 86 ASP cc_start: 0.9139 (m-30) cc_final: 0.8859 (m-30) REVERT: E 120 ASN cc_start: 0.8937 (p0) cc_final: 0.8038 (p0) REVERT: E 122 GLU cc_start: 0.8990 (tp30) cc_final: 0.8638 (pp20) REVERT: E 148 MET cc_start: 0.8119 (mmp) cc_final: 0.7881 (mmp) REVERT: E 234 GLU cc_start: 0.9105 (tp30) cc_final: 0.8498 (tp30) REVERT: E 283 LYS cc_start: 0.9422 (tmmt) cc_final: 0.9108 (tmmm) REVERT: E 288 PHE cc_start: 0.8551 (t80) cc_final: 0.8099 (t80) REVERT: E 353 LYS cc_start: 0.9259 (mmpt) cc_final: 0.8978 (mttt) REVERT: E 404 PHE cc_start: 0.7859 (m-80) cc_final: 0.7515 (m-10) REVERT: E 426 LEU cc_start: 0.9693 (tt) cc_final: 0.9464 (pp) REVERT: E 427 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8982 (pp) REVERT: E 448 MET cc_start: 0.9353 (tpt) cc_final: 0.8883 (tpt) REVERT: E 521 GLN cc_start: 0.9467 (tm-30) cc_final: 0.9148 (tm-30) REVERT: F 95 ARG cc_start: 0.8828 (mmt180) cc_final: 0.8505 (mmt180) REVERT: F 107 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8344 (mm-30) REVERT: F 254 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9409 (tt) REVERT: F 257 GLU cc_start: 0.8932 (tp30) cc_final: 0.8558 (mm-30) REVERT: F 314 ASP cc_start: 0.9040 (p0) cc_final: 0.8595 (p0) REVERT: F 345 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8283 (tm-30) REVERT: F 371 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8751 (mt-10) outliers start: 21 outliers final: 13 residues processed: 232 average time/residue: 1.1923 time to fit residues: 310.1181 Evaluate side-chains 232 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 22 optimal weight: 0.0770 chunk 41 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 132 optimal weight: 0.0970 chunk 8 optimal weight: 0.8980 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN B 162 GLN C 260 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.108804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.066128 restraints weight = 34289.939| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.89 r_work: 0.2651 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16702 Z= 0.180 Angle : 0.711 15.733 23063 Z= 0.344 Chirality : 0.044 0.440 2708 Planarity : 0.004 0.055 2618 Dihedral : 15.619 126.638 3559 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.20 % Allowed : 20.24 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 1.22 (0.20), residues: 1821 helix: 1.89 (0.17), residues: 926 sheet: -0.02 (0.33), residues: 231 loop : -0.39 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.003 TRP F 66 HIS 0.009 0.001 HIS E 152 PHE 0.010 0.001 PHE E 397 TYR 0.021 0.001 TYR F 135 ARG 0.006 0.000 ARG F 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6290.53 seconds wall clock time: 113 minutes 50.58 seconds (6830.58 seconds total)