Starting phenix.real_space_refine on Wed Nov 20 11:44:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b45_7049/11_2024/6b45_7049.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b45_7049/11_2024/6b45_7049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b45_7049/11_2024/6b45_7049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b45_7049/11_2024/6b45_7049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b45_7049/11_2024/6b45_7049.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b45_7049/11_2024/6b45_7049.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.714 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: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 17 5.16 5 C 13067 2.51 5 N 4065 2.21 5 O 4339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21547 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2079 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 310} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1373 Unresolved non-hydrogen angles: 1987 Unresolved non-hydrogen dihedrals: 884 Unresolved non-hydrogen chiralities: 392 Planarities with less than four sites: {'GLN:plan1': 29, 'ASP:plan': 20, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 9, 'HIS:plan': 9, 'PHE:plan': 11, 'GLU:plan': 24, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 726 Chain: "B" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2374 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2561 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2566 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2557 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 758 Classifications: {'peptide': 189} Incomplete info: {'backbone_only': 173, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 173} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 806 Unresolved non-hydrogen angles: 1152 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 12, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 10, 'GLU:plan': 11, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 414 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 11, 'rna3p_pur': 19, 'rna3p_pyr': 19} Link IDs: {'rna2p': 20, 'rna3p': 39} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 14.57, per 1000 atoms: 0.68 Number of scatterers: 21547 At special positions: 0 Unit cell: (158.76, 121.8, 150.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 59 15.00 O 4339 8.00 N 4065 7.00 C 13067 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: 4.95 Conformation dependent library (CDL) restraints added in 3.2 seconds 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4386 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 30 sheets defined 26.8% alpha, 12.4% beta 1 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 35 through 45 Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.553A pdb=" N ASP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.586A pdb=" N ILE A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS A 74 " --> pdb=" O LYS A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 74' Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 148 through 161 removed outlier: 3.674A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.864A pdb=" N PHE A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 294 through 306 Processing helix chain 'A' and resid 322 through 341 Processing helix chain 'A' and resid 354 through 360 removed outlier: 4.090A pdb=" N ALA A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 399 removed outlier: 3.715A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 4.017A pdb=" N SER A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.924A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.899A pdb=" N GLY B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.583A pdb=" N PHE B 152 " --> pdb=" O ASN B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 178 removed outlier: 3.619A pdb=" N ARG B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.643A pdb=" N LEU B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.761A pdb=" N LEU B 214 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.945A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.999A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 removed outlier: 4.024A pdb=" N GLN C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 191 through 205 removed outlier: 4.244A pdb=" N LEU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 263 removed outlier: 3.737A pdb=" N ALA C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 313 removed outlier: 4.250A pdb=" N ASP C 309 " --> pdb=" O TYR C 305 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN C 310 " --> pdb=" O THR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 removed outlier: 4.711A pdb=" N TYR C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.736A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 4.384A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 129 removed outlier: 3.876A pdb=" N GLN D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 144 removed outlier: 3.633A pdb=" N ASN D 141 " --> pdb=" O ARG D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 204 Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.844A pdb=" N ALA D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 removed outlier: 4.281A pdb=" N ASP D 309 " --> pdb=" O TYR D 305 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 removed outlier: 4.702A pdb=" N LEU D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 70 Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.554A pdb=" N ASP E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 144 removed outlier: 3.667A pdb=" N ARG E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 203 removed outlier: 4.069A pdb=" N LEU E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 263 Processing helix chain 'E' and resid 303 through 313 removed outlier: 4.531A pdb=" N ASP E 309 " --> pdb=" O TYR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 4.373A pdb=" N HIS E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL E 326 " --> pdb=" O GLN E 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.624A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 129 removed outlier: 3.690A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 191 through 205 removed outlier: 3.677A pdb=" N LEU F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 303 through 313 removed outlier: 3.894A pdb=" N ASP F 309 " --> pdb=" O TYR F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 333 removed outlier: 3.946A pdb=" N VAL F 326 " --> pdb=" O GLN F 322 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY F 333 " --> pdb=" O ASN F 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 66 through 71 Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.876A pdb=" N ARG G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 140 Processing helix chain 'G' and resid 191 through 205 removed outlier: 3.676A pdb=" N LEU G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 Processing helix chain 'G' and resid 303 through 308 removed outlier: 3.723A pdb=" N LEU G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 333 removed outlier: 4.138A pdb=" N VAL G 326 " --> pdb=" O GLN G 322 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 327 " --> pdb=" O GLN G 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.770A pdb=" N ALA H 35 " --> pdb=" O GLN H 32 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER H 36 " --> pdb=" O ARG H 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 32 through 36' Processing helix chain 'H' and resid 65 through 72 removed outlier: 3.639A pdb=" N GLN H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 129 removed outlier: 3.779A pdb=" N GLN H 120 " --> pdb=" O ASP H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 140 Processing helix chain 'H' and resid 192 through 204 Processing helix chain 'H' and resid 256 through 263 Processing helix chain 'H' and resid 303 through 313 removed outlier: 3.529A pdb=" N LEU H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 333 removed outlier: 4.320A pdb=" N HIS H 324 " --> pdb=" O VAL H 320 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL H 326 " --> pdb=" O GLN H 322 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 327 " --> pdb=" O GLN H 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 32 removed outlier: 4.320A pdb=" N LEU L 20 " --> pdb=" O PRO L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 77 removed outlier: 4.137A pdb=" N LEU L 76 " --> pdb=" O ARG L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 119 Processing helix chain 'L' and resid 123 through 130 removed outlier: 4.126A pdb=" N ALA L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.752A pdb=" N THR A 69 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.602A pdb=" N PHE A 180 " --> pdb=" O HIS A 188 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS A 188 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.602A pdb=" N PHE A 180 " --> pdb=" O HIS A 188 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS A 188 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.544A pdb=" N ASN A 262 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 16 removed outlier: 3.527A pdb=" N VAL B 107 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS B 104 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU B 67 " --> pdb=" O HIS B 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.532A pdb=" N ARG C 98 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL C 93 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA C 215 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 24 through 28 removed outlier: 4.905A pdb=" N VAL C 93 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA C 215 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 266 through 268 removed outlier: 5.060A pdb=" N ILE C 280 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.941A pdb=" N LEU D 12 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.795A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 217 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA D 157 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.795A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 255 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 49 removed outlier: 3.713A pdb=" N VAL D 49 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA D 82 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 287 through 288 Processing sheet with id=AB6, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.547A pdb=" N ARG E 94 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 24 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.638A pdb=" N GLU E 212 " --> pdb=" O ASN E 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 49 removed outlier: 3.558A pdb=" N GLN E 77 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 248 through 249 Processing sheet with id=AC1, first strand: chain 'E' and resid 266 through 268 removed outlier: 5.257A pdb=" N ILE E 280 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.605A pdb=" N LEU F 12 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 170 through 175 removed outlier: 4.384A pdb=" N ARG F 172 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU F 159 " --> pdb=" O PHE F 216 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE F 216 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL F 99 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 45 through 51 removed outlier: 3.526A pdb=" N VAL F 49 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY F 51 " --> pdb=" O ASN F 75 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN F 75 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AC6, first strand: chain 'G' and resid 18 through 20 removed outlier: 4.290A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU G 212 " --> pdb=" O ASN G 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN G 163 " --> pdb=" O GLU G 212 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU G 159 " --> pdb=" O PHE G 216 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.783A pdb=" N ARG G 94 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU G 24 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA G 253 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 45 through 50 removed outlier: 8.232A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 12 through 13 removed outlier: 3.921A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 24 through 26 removed outlier: 3.575A pdb=" N VAL H 99 " --> pdb=" O VAL H 209 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL H 209 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU H 212 " --> pdb=" O ASN H 163 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL H 160 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG H 175 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE H 162 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA H 173 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS H 164 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.611A pdb=" N VAL H 81 " --> pdb=" O ARG H 45 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 49 through 50 623 hydrogen bonds defined for protein. 1737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 5.75 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: 6363 1.33 - 1.45: 4315 1.45 - 1.58: 11233 1.58 - 1.70: 118 1.70 - 1.82: 25 Bond restraints: 22054 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.334 1.380 -0.046 8.40e-03 1.42e+04 2.99e+01 bond pdb=" C ASP G 63 " pdb=" N PRO G 64 " ideal model delta sigma weight residual 1.334 1.355 -0.022 8.40e-03 1.42e+04 6.77e+00 bond pdb=" CB ASN C 262 " pdb=" CG ASN C 262 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.37e+00 bond pdb=" N VAL H 225 " pdb=" CA VAL H 225 " ideal model delta sigma weight residual 1.459 1.439 0.020 1.25e-02 6.40e+03 2.54e+00 bond pdb=" CG1 ILE F 260 " pdb=" CD1 ILE F 260 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.42e+00 ... (remaining 22049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 29319 2.93 - 5.86: 596 5.86 - 8.79: 73 8.79 - 11.72: 18 11.72 - 14.65: 4 Bond angle restraints: 30010 Sorted by residual: angle pdb=" N ILE D 327 " pdb=" CA ILE D 327 " pdb=" C ILE D 327 " ideal model delta sigma weight residual 113.53 104.84 8.69 9.80e-01 1.04e+00 7.87e+01 angle pdb=" N LYS F 60 " pdb=" CA LYS F 60 " pdb=" C LYS F 60 " ideal model delta sigma weight residual 114.31 106.67 7.64 1.29e+00 6.01e-01 3.51e+01 angle pdb=" C ALA G 319 " pdb=" N VAL G 320 " pdb=" CA VAL G 320 " ideal model delta sigma weight residual 121.97 131.57 -9.60 1.80e+00 3.09e-01 2.85e+01 angle pdb=" C ARG E 250 " pdb=" N ASP E 251 " pdb=" CA ASP E 251 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" N VAL E 249 " pdb=" CA VAL E 249 " pdb=" C VAL E 249 " ideal model delta sigma weight residual 109.34 98.62 10.72 2.08e+00 2.31e-01 2.65e+01 ... (remaining 30005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.94: 12125 29.94 - 59.88: 385 59.88 - 89.81: 83 89.81 - 119.75: 7 119.75 - 149.69: 2 Dihedral angle restraints: 12602 sinusoidal: 5288 harmonic: 7314 Sorted by residual: dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 50.31 149.69 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 52.71 147.29 1 1.50e+01 4.44e-03 7.86e+01 dihedral pdb=" CA SER A 227 " pdb=" C SER A 227 " pdb=" N TRP A 228 " pdb=" CA TRP A 228 " ideal model delta harmonic sigma weight residual 180.00 138.75 41.25 0 5.00e+00 4.00e-02 6.81e+01 ... (remaining 12599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2663 0.081 - 0.162: 404 0.162 - 0.243: 41 0.243 - 0.324: 3 0.324 - 0.405: 3 Chirality restraints: 3114 Sorted by residual: chirality pdb=" CB ILE F 232 " pdb=" CA ILE F 232 " pdb=" CG1 ILE F 232 " pdb=" CG2 ILE F 232 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C1' C M 1 " pdb=" O4' C M 1 " pdb=" C2' C M 1 " pdb=" N1 C M 1 " both_signs ideal model delta sigma weight residual False 2.46 2.06 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CB ILE F 165 " pdb=" CA ILE F 165 " pdb=" CG1 ILE F 165 " pdb=" CG2 ILE F 165 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 3111 not shown) Planarity restraints: 3899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 324 " -0.026 2.00e-02 2.50e+03 3.27e-02 1.60e+01 pdb=" CG HIS C 324 " 0.070 2.00e-02 2.50e+03 pdb=" ND1 HIS C 324 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS C 324 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 HIS C 324 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 324 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 152 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO B 153 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 153 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 153 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 63 " 0.049 5.00e-02 4.00e+02 7.47e-02 8.94e+00 pdb=" N PRO G 64 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO G 64 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 64 " 0.042 5.00e-02 4.00e+02 ... (remaining 3896 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4171 2.77 - 3.30: 18783 3.30 - 3.84: 35286 3.84 - 4.37: 39895 4.37 - 4.90: 67913 Nonbonded interactions: 166048 Sorted by model distance: nonbonded pdb=" OG SER C 290 " pdb=" O ASP L 12 " model vdw 2.240 3.040 nonbonded pdb=" OG SER C 86 " pdb=" OD2 ASP C 221 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR G 271 " pdb=" O GLY G 278 " model vdw 2.264 3.040 nonbonded pdb=" OE1 GLU C 230 " pdb=" OG SER D 48 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR G 305 " pdb=" O SER H 54 " model vdw 2.304 3.040 ... (remaining 166043 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 'C' and (resid 6 through 272 or (resid 273 through 275 and (name N or nam \ e CA or name C or name O or name CB )) or resid 276 through 338)) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 50.720 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 22054 Z= 0.371 Angle : 1.046 14.649 30010 Z= 0.560 Chirality : 0.059 0.405 3114 Planarity : 0.006 0.075 3899 Dihedral : 14.876 149.689 8216 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.26 % Favored : 87.64 % Rotamer: Outliers : 0.65 % Allowed : 4.55 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.15 % 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: -5.05 (0.12), residues: 2855 helix: -3.63 (0.11), residues: 768 sheet: -2.46 (0.25), residues: 361 loop : -3.59 (0.12), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP E 311 HIS 0.041 0.003 HIS C 324 PHE 0.043 0.004 PHE F 95 TYR 0.030 0.003 TYR E 138 ARG 0.014 0.001 ARG G 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 335 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.6893 (tp-100) cc_final: 0.5722 (pt0) REVERT: B 21 ASN cc_start: 0.7699 (t0) cc_final: 0.7193 (p0) REVERT: B 160 LEU cc_start: 0.5634 (mp) cc_final: 0.5188 (tt) REVERT: B 170 ARG cc_start: 0.6206 (mtt180) cc_final: 0.5669 (ptm160) REVERT: C 218 ARG cc_start: 0.4067 (mtp180) cc_final: 0.2980 (tmt170) REVERT: C 316 GLU cc_start: 0.6459 (mm-30) cc_final: 0.6093 (tm-30) REVERT: D 290 SER cc_start: 0.8031 (m) cc_final: 0.7335 (t) REVERT: F 58 LYS cc_start: 0.7334 (tttt) cc_final: 0.7113 (mmtt) REVERT: G 75 ASN cc_start: 0.6646 (p0) cc_final: 0.6432 (p0) REVERT: G 76 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7427 (tt) REVERT: H 271 TYR cc_start: 0.7058 (p90) cc_final: 0.6733 (p90) outliers start: 12 outliers final: 1 residues processed: 343 average time/residue: 0.2423 time to fit residues: 123.6261 Evaluate side-chains 197 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 195 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain G residue 76 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 138 optimal we------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS B 82 ASN B 114 HIS ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS C 140 HIS C 141 ASN ** C 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 164 HIS ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN F 75 ASN F 223 GLN G 129 GLN ** G 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS H 151 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22054 Z= 0.280 Angle : 0.709 10.038 30010 Z= 0.373 Chirality : 0.046 0.283 3114 Planarity : 0.006 0.068 3899 Dihedral : 16.010 147.747 4055 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 2.65 % Allowed : 10.51 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.11 (0.13), residues: 2855 helix: -2.39 (0.15), residues: 771 sheet: -2.03 (0.25), residues: 371 loop : -3.20 (0.13), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 311 HIS 0.017 0.002 HIS C 324 PHE 0.033 0.002 PHE E 226 TYR 0.021 0.002 TYR E 114 ARG 0.006 0.001 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.7421 (mt) cc_final: 0.6841 (tt) REVERT: A 241 GLN cc_start: 0.6996 (tp-100) cc_final: 0.5847 (pt0) REVERT: B 160 LEU cc_start: 0.5496 (mp) cc_final: 0.5257 (tt) REVERT: B 170 ARG cc_start: 0.6443 (mtt180) cc_final: 0.5680 (mmm160) REVERT: C 167 GLN cc_start: 0.4922 (OUTLIER) cc_final: 0.4264 (pm20) REVERT: C 218 ARG cc_start: 0.4000 (mtp180) cc_final: 0.2841 (tmt170) REVERT: C 316 GLU cc_start: 0.6282 (mm-30) cc_final: 0.5977 (tm-30) REVERT: D 290 SER cc_start: 0.7751 (m) cc_final: 0.7443 (m) REVERT: E 127 ASN cc_start: 0.7334 (m110) cc_final: 0.7127 (m110) REVERT: E 208 HIS cc_start: 0.5988 (t-90) cc_final: 0.5504 (t-90) REVERT: H 271 TYR cc_start: 0.7049 (p90) cc_final: 0.6749 (p90) outliers start: 49 outliers final: 31 residues processed: 256 average time/residue: 0.2485 time to fit residues: 99.6515 Evaluate side-chains 209 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 303 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 179 optimal weight: 8.9990 chunk 72 optimal weight: 40.0000 chunk 263 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: