Starting phenix.real_space_refine on Sun Feb 18 14:22:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b47_7051/02_2024/6b47_7051.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b47_7051/02_2024/6b47_7051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b47_7051/02_2024/6b47_7051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b47_7051/02_2024/6b47_7051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b47_7051/02_2024/6b47_7051.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b47_7051/02_2024/6b47_7051.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 20 5.16 5 C 13479 2.51 5 N 4171 2.21 5 O 4484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22213 Number of models: 1 Model: "" Number of chains: 11 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: 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: "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: 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: "K" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 668 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} 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': 9, 'rna2p_pyr': 11, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 19, 'rna3p': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 12.26, per 1000 atoms: 0.55 Number of scatterers: 22213 At special positions: 0 Unit cell: (152.281, 122.254, 153.353, 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 20 16.00 P 59 15.00 O 4484 8.00 N 4171 7.00 C 13479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.34 Conformation dependent library (CDL) restraints added in 4.4 seconds 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4550 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 47 sheets defined 32.3% alpha, 19.5% beta 1 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 7.76 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 removed outlier: 3.737A pdb=" N LYS A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.975A pdb=" N HIS A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 removed outlier: 4.242A pdb=" N ARG A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.559A pdb=" N GLU A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 100 " --> pdb=" O SER A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 100' Processing helix chain 'A' and resid 114 through 122 removed outlier: 3.805A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 317 through 341 removed outlier: 3.523A pdb=" N ARG A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 384 through 397 Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.928A pdb=" N LEU A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 434 removed outlier: 3.869A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.951A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.685A pdb=" N LEU B 118 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 115 through 119' Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.638A pdb=" N LEU B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.839A pdb=" N GLU C 38 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP C 39 " --> pdb=" O SER C 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 35 through 39' Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 189 through 205 Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.671A pdb=" N ILE C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.502A pdb=" N GLN D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.514A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.582A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 314 removed outlier: 3.624A pdb=" N ARG D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'E' and resid 32 through 39 removed outlier: 3.682A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLN E 37 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TRP E 39 " --> pdb=" O SER E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 Processing helix chain 'E' and resid 112 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.622A pdb=" N ARG E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.610A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 73 removed outlier: 3.639A pdb=" N SER F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 3.561A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 190 through 204 removed outlier: 3.754A pdb=" N SER F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.555A pdb=" N ILE F 260 " --> pdb=" O HIS F 256 " (cutoff:3.500A) 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 303 through 313 Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.527A pdb=" N SER G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 190 through 205 removed outlier: 3.510A pdb=" N GLY G 205 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 265 removed outlier: 3.528A pdb=" N ILE G 260 " --> pdb=" O HIS G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.513A pdb=" N SER H 36 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 73 removed outlier: 4.142A pdb=" N SER H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 189 through 204 Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.527A pdb=" N ILE H 260 " --> pdb=" O HIS H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 278 Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'K' and resid 9 through 19 Processing helix chain 'K' and resid 57 through 68 Processing helix chain 'K' and resid 76 through 81 Processing helix chain 'K' and resid 81 through 86 Processing helix chain 'L' and resid 16 through 32 Processing helix chain 'L' and resid 33 through 35 No H-bonds generated for 'chain 'L' and resid 33 through 35' Processing helix chain 'L' and resid 67 through 71 removed outlier: 3.785A pdb=" N LEU L 70 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU L 71 " --> pdb=" O ARG L 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 67 through 71' Processing helix chain 'L' and resid 111 through 119 Processing helix chain 'L' and resid 123 through 131 removed outlier: 3.563A pdb=" N ALA L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 8.610A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 187 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 8.610A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 251 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232 removed outlier: 3.631A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 219 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 60 removed outlier: 5.773A pdb=" N GLY B 112 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.585A pdb=" N ARG B 65 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.634A pdb=" N ALA C 108 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 12 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 20 removed outlier: 4.533A pdb=" N VAL C 209 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 44 through 47 removed outlier: 3.616A pdb=" N LYS C 47 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 79 " --> pdb=" O LYS C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 229 through 230 removed outlier: 4.156A pdb=" N THR C 245 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 248 through 249 removed outlier: 3.723A pdb=" N ALA C 252 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 266 through 268 removed outlier: 3.770A pdb=" N ILE C 280 " --> pdb=" O ASP C 268 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.587A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.497A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 160 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG D 175 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE D 162 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA D 173 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS D 164 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'D' and resid 45 through 51 removed outlier: 3.991A pdb=" N GLY D 51 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN D 75 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 229 through 230 removed outlier: 4.539A pdb=" N THR D 245 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.579A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.574A pdb=" N LEU E 12 " --> pdb=" O PHE E 336 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.541A pdb=" N VAL E 99 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE E 162 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AC5, 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: 4.458A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 252 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 50 Processing sheet with id=AC7, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AC8, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AC9, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.581A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 12 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.492A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA F 157 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL F 158 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP F 177 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE F 162 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AD3, first strand: chain 'F' and resid 45 through 50 removed outlier: 4.572A pdb=" N ALA F 82 " --> pdb=" O VAL F 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AD5, first strand: chain 'F' and resid 287 through 288 Processing sheet with id=AD6, first strand: chain 'G' and resid 12 through 14 Processing sheet with id=AD7, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.352A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL G 160 " --> pdb=" O PHE G 176 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.861A pdb=" N ALA G 253 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 45 through 50 removed outlier: 4.502A pdb=" N ALA G 82 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 45 through 50 removed outlier: 7.618A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.804A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 19 through 20 removed outlier: 4.456A pdb=" N VAL H 209 " --> pdb=" O VAL H 99 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 170 through 177 removed outlier: 3.557A pdb=" N ARG H 172 " --> pdb=" O HIS H 164 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA H 253 " --> pdb=" O MET H 25 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 249 " --> pdb=" O ALA H 252 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 44 through 50 removed outlier: 4.413A pdb=" N ALA H 82 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 44 through 50 removed outlier: 7.524A pdb=" N SER H 243 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR H 78 " --> pdb=" O SER H 243 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AE8, first strand: chain 'H' and resid 287 through 288 Processing sheet with id=AE9, first strand: chain 'K' and resid 23 through 27 Processing sheet with id=AF1, first strand: chain 'K' and resid 41 through 46 removed outlier: 3.628A pdb=" N ILE K 44 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 5 through 6 926 hydrogen bonds defined for protein. 2586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 7.87 Time building geometry restraints manager: 9.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4584 1.32 - 1.45: 5677 1.45 - 1.57: 12320 1.57 - 1.69: 118 1.69 - 1.81: 30 Bond restraints: 22729 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.331 1.364 -0.033 7.90e-03 1.60e+04 1.72e+01 bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.339 1.448 -0.109 3.40e-02 8.65e+02 1.03e+01 bond pdb=" CG1 ILE E 260 " pdb=" CD1 ILE E 260 " ideal model delta sigma weight residual 1.513 1.402 0.111 3.90e-02 6.57e+02 8.09e+00 bond pdb=" CG1 ILE F 260 " pdb=" CD1 ILE F 260 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.31e+00 bond pdb=" C ARG B 85 " pdb=" N ASN B 86 " ideal model delta sigma weight residual 1.329 1.281 0.048 1.86e-02 2.89e+03 6.66e+00 ... (remaining 22724 not shown) Histogram of bond angle deviations from ideal: 96.37 - 103.92: 420 103.92 - 111.48: 9312 111.48 - 119.03: 8585 119.03 - 126.59: 12147 126.59 - 134.14: 458 Bond angle restraints: 30922 Sorted by residual: angle pdb=" N GLN G 37 " pdb=" CA GLN G 37 " pdb=" C GLN G 37 " ideal model delta sigma weight residual 114.56 106.99 7.57 1.27e+00 6.20e-01 3.55e+01 angle pdb=" C SER A 252 " pdb=" N GLN A 253 " pdb=" CA GLN A 253 " ideal model delta sigma weight residual 122.08 130.02 -7.94 1.47e+00 4.63e-01 2.91e+01 angle pdb=" C LYS H 58 " pdb=" N THR H 59 " pdb=" CA THR H 59 " ideal model delta sigma weight residual 122.61 129.57 -6.96 1.56e+00 4.11e-01 1.99e+01 angle pdb=" C GLN G 32 " pdb=" N ARG G 33 " pdb=" CA ARG G 33 " ideal model delta sigma weight residual 120.38 126.82 -6.44 1.46e+00 4.69e-01 1.95e+01 angle pdb=" N GLN D 167 " pdb=" CA GLN D 167 " pdb=" C GLN D 167 " ideal model delta sigma weight residual 108.07 102.02 6.05 1.38e+00 5.25e-01 1.92e+01 ... (remaining 30917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 12665 32.59 - 65.18: 313 65.18 - 97.77: 29 97.77 - 130.36: 0 130.36 - 162.95: 2 Dihedral angle restraints: 13009 sinusoidal: 5442 harmonic: 7567 Sorted by residual: 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 37.05 162.95 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" CA TYR E 285 " pdb=" C TYR E 285 " pdb=" N GLY E 286 " pdb=" CA GLY E 286 " ideal model delta harmonic sigma weight residual 180.00 -136.39 -43.61 0 5.00e+00 4.00e-02 7.61e+01 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 69.00 131.00 1 1.50e+01 4.44e-03 7.07e+01 ... (remaining 13006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2633 0.076 - 0.152: 539 0.152 - 0.228: 38 0.228 - 0.304: 3 0.304 - 0.381: 2 Chirality restraints: 3215 Sorted by residual: chirality pdb=" CB ILE H 267 " pdb=" CA ILE H 267 " pdb=" CG1 ILE H 267 " pdb=" CG2 ILE H 267 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB ILE F 267 " pdb=" CA ILE F 267 " pdb=" CG1 ILE F 267 " pdb=" CG2 ILE F 267 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C1' U M 21 " pdb=" O4' U M 21 " pdb=" C2' U M 21 " pdb=" N1 U M 21 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3212 not shown) Planarity restraints: 4018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 311 " -0.030 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP E 311 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP E 311 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP E 311 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 311 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 311 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 311 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 311 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 311 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 311 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 311 " -0.028 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP D 311 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP D 311 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 311 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 311 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 311 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 311 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 311 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 311 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 311 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 311 " 0.027 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP G 311 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP G 311 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 311 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 311 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP G 311 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP G 311 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 311 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 311 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP G 311 " 0.001 2.00e-02 2.50e+03 ... (remaining 4015 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 69 2.44 - 3.05: 12847 3.05 - 3.67: 33056 3.67 - 4.28: 49300 4.28 - 4.90: 83178 Nonbonded interactions: 178450 Sorted by model distance: nonbonded pdb=" CE MET K 1 " pdb=" NE2 GLN K 4 " model vdw 1.819 3.540 nonbonded pdb=" CB ALA L 0 " pdb=" N GLU L 170 " model vdw 2.133 3.540 nonbonded pdb=" CE MET K 1 " pdb=" CD GLN K 4 " model vdw 2.271 3.690 nonbonded pdb=" OH TYR E 305 " pdb=" O SER F 54 " model vdw 2.278 2.440 nonbonded pdb=" O GLU E 283 " pdb=" OH TYR E 325 " model vdw 2.285 2.440 ... (remaining 178445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '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 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: 0.650 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: 0.030 Extract box with map and model: 4.140 Check model and map are aligned: 0.310 Set scattering table: 0.240 Process input model: 65.650 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 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 : 0.009 0.111 22729 Z= 0.606 Angle : 1.034 11.348 30922 Z= 0.570 Chirality : 0.059 0.381 3215 Planarity : 0.006 0.061 4018 Dihedral : 13.370 162.947 8459 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.65 % Favored : 89.18 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.03 (0.12), residues: 2939 helix: -2.54 (0.13), residues: 885 sheet: -1.24 (0.24), residues: 439 loop : -3.29 (0.12), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.006 TRP E 311 HIS 0.020 0.004 HIS F 164 PHE 0.027 0.004 PHE C 216 TYR 0.036 0.004 TYR D 305 ARG 0.018 0.002 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 ARG cc_start: 0.6502 (ttm110) cc_final: 0.6270 (ttm110) REVERT: B 108 SER cc_start: 0.7328 (m) cc_final: 0.6689 (p) REVERT: B 116 ASP cc_start: 0.5717 (p0) cc_final: 0.5095 (m-30) REVERT: C 124 THR cc_start: 0.8030 (m) cc_final: 0.7277 (m) REVERT: D 221 ASP cc_start: 0.7063 (m-30) cc_final: 0.6862 (m-30) REVERT: D 302 LEU cc_start: 0.7323 (mt) cc_final: 0.7005 (mt) REVERT: G 119 LEU cc_start: 0.8563 (mt) cc_final: 0.8326 (mt) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.4066 time to fit residues: 289.3298 Evaluate side-chains 237 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 2.9990 chunk 225 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS B 42 HIS C 129 GLN C 164 HIS D 164 HIS D 223 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS E 223 GLN F 75 ASN F 110 ASN F 164 HIS F 291 GLN H 32 GLN H 129 GLN H 164 HIS K 45 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 22729 Z= 0.354 Angle : 0.722 11.565 30922 Z= 0.385 Chirality : 0.045 0.177 3215 Planarity : 0.006 0.083 4018 Dihedral : 14.321 159.854 4141 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.57 % Favored : 91.36 % Rotamer: Outliers : 1.83 % Allowed : 9.61 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.55 (0.14), residues: 2939 helix: -0.60 (0.16), residues: 906 sheet: -0.31 (0.24), residues: 437 loop : -2.90 (0.13), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 311 HIS 0.010 0.002 HIS H 164 PHE 0.024 0.002 PHE B 184 TYR 0.022 0.002 TYR K 64 ARG 0.012 0.001 ARG C 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 HIS cc_start: 0.7831 (t70) cc_final: 0.7575 (t70) REVERT: A 241 GLN cc_start: 0.8528 (tt0) cc_final: 0.8093 (tt0) REVERT: B 159 LEU cc_start: 0.7711 (tt) cc_final: 0.7114 (tt) REVERT: C 247 TYR cc_start: 0.7486 (t80) cc_final: 0.7272 (t80) REVERT: F 26 SER cc_start: 0.9324 (p) cc_final: 0.8958 (m) REVERT: H 119 LEU cc_start: 0.8780 (mm) cc_final: 0.8461 (mm) REVERT: H 271 TYR cc_start: 0.8658 (p90) cc_final: 0.8454 (p90) outliers start: 35 outliers final: 19 residues processed: 243 average time/residue: 0.4495 time to fit residues: 160.2143 Evaluate side-chains 168 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 0.0370 chunk 83 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 chunk 292 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN H 72 GLN H 223 GLN K 45 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22729 Z= 0.208 Angle : 0.572 13.265 30922 Z= 0.302 Chirality : 0.041 0.250 3215 Planarity : 0.004 0.038 4018 Dihedral : 13.997 158.695 4141 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.00 % Favored : 91.94 % Rotamer: Outliers : 2.14 % Allowed : 11.70 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.62 (0.15), residues: 2939 helix: 0.54 (0.17), residues: 917 sheet: 0.14 (0.25), residues: 435 loop : -2.57 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 311 HIS 0.020 0.001 HIS A 203 PHE 0.015 0.001 PHE B 184 TYR 0.018 0.002 TYR C 114 ARG 0.010 0.001 ARG H 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 176 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 GLN cc_start: 0.8583 (tt0) cc_final: 0.8215 (tt0) REVERT: B 99 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: B 281 GLU cc_start: 0.5794 (mt-10) cc_final: 0.5273 (mt-10) REVERT: D 67 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8510 (tt) REVERT: E 74 PRO cc_start: 0.7943 (Cg_endo) cc_final: 0.7729 (Cg_exo) REVERT: G 22 ASP cc_start: 0.8562 (m-30) cc_final: 0.8342 (m-30) REVERT: H 119 LEU cc_start: 0.8848 (mm) cc_final: 0.8442 (mm) REVERT: H 271 TYR cc_start: 0.8703 (p90) cc_final: 0.8388 (p90) outliers start: 41 outliers final: 22 residues processed: 208 average time/residue: 0.4143 time to fit residues: 126.9804 Evaluate side-chains 159 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 30 optimal weight: 50.0000 chunk 129 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 chunk 288 optimal weight: 50.0000 chunk 142 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 306 HIS F 75 ASN G 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22729 Z= 0.332 Angle : 0.626 12.898 30922 Z= 0.331 Chirality : 0.043 0.216 3215 Planarity : 0.004 0.039 4018 Dihedral : 13.970 159.635 4141 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.08 % Favored : 90.85 % Rotamer: Outliers : 2.45 % Allowed : 12.53 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.15), residues: 2939 helix: 0.87 (0.17), residues: 917 sheet: 0.26 (0.25), residues: 450 loop : -2.43 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 311 HIS 0.005 0.001 HIS G 256 PHE 0.018 0.002 PHE B 184 TYR 0.020 0.002 TYR A 235 ARG 0.005 0.001 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.6005 (pm20) cc_final: 0.5713 (pm20) REVERT: A 241 GLN cc_start: 0.8647 (tt0) cc_final: 0.8350 (tt0) REVERT: B 99 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: B 281 GLU cc_start: 0.5944 (mt-10) cc_final: 0.5610 (mt-10) REVERT: D 50 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7090 (ptt180) REVERT: E 74 PRO cc_start: 0.8284 (Cg_endo) cc_final: 0.8075 (Cg_exo) REVERT: E 277 LEU cc_start: 0.7176 (mp) cc_final: 0.6968 (mp) REVERT: E 283 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: G 285 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7761 (p90) REVERT: H 271 TYR cc_start: 0.8769 (p90) cc_final: 0.8481 (p90) outliers start: 47 outliers final: 34 residues processed: 193 average time/residue: 0.3985 time to fit residues: 114.1797 Evaluate side-chains 176 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 129 GLN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 38 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 118 optimal weight: 0.0000 chunk 245 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 0 optimal weight: 70.0000 chunk 147 optimal weight: 0.5980 chunk 258 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS B 18 GLN B 282 ASN C 83 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.7036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22729 Z= 0.155 Angle : 0.520 11.455 30922 Z= 0.275 Chirality : 0.040 0.258 3215 Planarity : 0.003 0.045 4018 Dihedral : 13.791 157.927 4141 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.98 % Favored : 92.96 % Rotamer: Outliers : 1.98 % Allowed : 13.68 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2939 helix: 1.31 (0.18), residues: 929 sheet: 0.45 (0.26), residues: 425 loop : -2.26 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 174 HIS 0.005 0.001 HIS B 306 PHE 0.013 0.001 PHE A 211 TYR 0.022 0.001 TYR C 114 ARG 0.009 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.6735 (mmm-85) cc_final: 0.6400 (mmm-85) REVERT: A 241 GLN cc_start: 0.8586 (tt0) cc_final: 0.8373 (tt0) REVERT: C 293 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7926 (tmtt) REVERT: D 50 ARG cc_start: 0.7447 (ttp80) cc_final: 0.7087 (ptt180) REVERT: E 74 PRO cc_start: 0.8102 (Cg_endo) cc_final: 0.7866 (Cg_exo) REVERT: G 241 GLN cc_start: 0.7618 (pm20) cc_final: 0.7296 (tt0) REVERT: H 271 TYR cc_start: 0.8672 (p90) cc_final: 0.8359 (p90) outliers start: 38 outliers final: 25 residues processed: 189 average time/residue: 0.4199 time to fit residues: 116.5907 Evaluate side-chains 158 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 56 optimal weight: 0.0000 chunk 169 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 288 optimal weight: 50.0000 chunk 239 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 18 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN C 129 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.7252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22729 Z= 0.304 Angle : 0.588 11.475 30922 Z= 0.310 Chirality : 0.042 0.224 3215 Planarity : 0.004 0.038 4018 Dihedral : 13.819 158.195 4141 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.88 % Favored : 91.05 % Rotamer: Outliers : 2.56 % Allowed : 13.68 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2939 helix: 1.39 (0.18), residues: 919 sheet: 0.38 (0.25), residues: 436 loop : -2.21 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 30 HIS 0.006 0.001 HIS B 306 PHE 0.014 0.002 PHE B 184 TYR 0.018 0.002 TYR C 271 ARG 0.007 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 134 time to evaluate : 2.366 Fit side-chains revert: symmetry clash REVERT: A 222 ARG cc_start: 0.6843 (mmm-85) cc_final: 0.6451 (mmm-85) REVERT: B 99 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: D 50 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7173 (ptt180) REVERT: E 74 PRO cc_start: 0.8182 (Cg_endo) cc_final: 0.7972 (Cg_exo) REVERT: G 33 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8687 (ptt-90) REVERT: H 271 TYR cc_start: 0.8775 (p90) cc_final: 0.8440 (p90) outliers start: 49 outliers final: 36 residues processed: 171 average time/residue: 0.4283 time to fit residues: 106.9968 Evaluate side-chains 168 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 232 ILE Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 50.0000 chunk 32 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 163 optimal weight: 0.3980 chunk 242 optimal weight: 7.9990 chunk 161 optimal weight: 0.0980 chunk 287 optimal weight: 50.0000 chunk 179 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 chunk 132 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS H 164 HIS K 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.7421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22729 Z= 0.128 Angle : 0.497 10.552 30922 Z= 0.261 Chirality : 0.039 0.234 3215 Planarity : 0.003 0.041 4018 Dihedral : 13.694 156.725 4141 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.83 % Allowed : 14.62 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2939 helix: 1.71 (0.18), residues: 936 sheet: 0.50 (0.25), residues: 428 loop : -2.10 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP K 67 HIS 0.004 0.001 HIS B 196 PHE 0.009 0.001 PHE B 184 TYR 0.022 0.001 TYR C 305 ARG 0.006 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.6714 (mmm-85) cc_final: 0.5791 (mpt180) REVERT: B 99 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: C 170 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8314 (p) REVERT: D 50 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7028 (ptt180) REVERT: F 295 TYR cc_start: 0.8571 (m-80) cc_final: 0.8333 (m-80) REVERT: G 241 GLN cc_start: 0.7598 (pm20) cc_final: 0.7291 (tt0) REVERT: H 271 TYR cc_start: 0.8713 (p90) cc_final: 0.8358 (p90) REVERT: K 32 TYR cc_start: 0.8182 (m-10) cc_final: 0.7622 (m-80) outliers start: 35 outliers final: 24 residues processed: 177 average time/residue: 0.4130 time to fit residues: 107.8421 Evaluate side-chains 161 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 147 TRP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain K residue 42 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 0.0870 chunk 114 optimal weight: 4.9990 chunk 171 optimal weight: 0.0030 chunk 86 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 142 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 chunk 225 optimal weight: 0.6980 overall best weight: 0.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN C 140 HIS ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.7571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22729 Z= 0.118 Angle : 0.476 11.777 30922 Z= 0.250 Chirality : 0.038 0.216 3215 Planarity : 0.003 0.037 4018 Dihedral : 13.599 156.507 4141 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.41 % Allowed : 15.46 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2939 helix: 2.05 (0.18), residues: 930 sheet: 0.44 (0.25), residues: 445 loop : -2.01 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 67 HIS 0.005 0.001 HIS B 196 PHE 0.011 0.001 PHE C 304 TYR 0.020 0.001 TYR C 305 ARG 0.006 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ARG cc_start: 0.6738 (mmm-85) cc_final: 0.5807 (mpt180) REVERT: B 99 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: C 170 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8110 (p) REVERT: D 50 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7255 (ptt180) REVERT: F 38 GLU cc_start: 0.7472 (pp20) cc_final: 0.6849 (pp20) REVERT: F 295 TYR cc_start: 0.8516 (m-80) cc_final: 0.8270 (m-80) REVERT: G 241 GLN cc_start: 0.7507 (pm20) cc_final: 0.7193 (mt0) REVERT: H 259 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7419 (ptmt) REVERT: H 271 TYR cc_start: 0.8601 (p90) cc_final: 0.8294 (p90) outliers start: 27 outliers final: 17 residues processed: 189 average time/residue: 0.4008 time to fit residues: 113.2146 Evaluate side-chains 160 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 221 ASP Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 3.9990 chunk 275 optimal weight: 20.0000 chunk 251 optimal weight: 0.1980 chunk 267 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 266 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS C 83 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.7603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22729 Z= 0.223 Angle : 0.534 12.429 30922 Z= 0.281 Chirality : 0.040 0.204 3215 Planarity : 0.003 0.045 4018 Dihedral : 13.655 156.649 4141 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.25 % Allowed : 15.87 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2939 helix: 1.95 (0.18), residues: 930 sheet: 0.64 (0.25), residues: 435 loop : -1.99 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP B 147 HIS 0.005 0.001 HIS B 196 PHE 0.010 0.001 PHE B 184 TYR 0.024 0.002 TYR C 305 ARG 0.006 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8260 (mmmt) REVERT: B 99 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: C 283 GLU cc_start: 0.7882 (pm20) cc_final: 0.7279 (pm20) REVERT: D 50 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7339 (ptt180) REVERT: E 74 PRO cc_start: 0.8304 (Cg_endo) cc_final: 0.8072 (Cg_exo) REVERT: G 241 GLN cc_start: 0.7560 (pm20) cc_final: 0.7267 (tt0) REVERT: H 259 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.6803 (ptmt) REVERT: H 271 TYR cc_start: 0.8673 (p90) cc_final: 0.8329 (p90) outliers start: 24 outliers final: 18 residues processed: 156 average time/residue: 0.4329 time to fit residues: 100.1383 Evaluate side-chains 149 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 1.9990 chunk 283 optimal weight: 50.0000 chunk 172 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 296 optimal weight: 40.0000 chunk 273 optimal weight: 0.9980 chunk 236 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.7683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22729 Z= 0.165 Angle : 0.513 12.017 30922 Z= 0.270 Chirality : 0.039 0.199 3215 Planarity : 0.003 0.035 4018 Dihedral : 13.602 156.403 4141 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.25 % Allowed : 16.08 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2939 helix: 2.05 (0.18), residues: 929 sheet: 0.63 (0.25), residues: 446 loop : -1.95 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP B 147 HIS 0.005 0.001 HIS B 196 PHE 0.009 0.001 PHE B 184 TYR 0.022 0.001 TYR C 305 ARG 0.006 0.000 ARG C 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5878 Ramachandran restraints generated. 2939 Oldfield, 0 Emsley, 2939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: C 170 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8420 (p) REVERT: C 283 GLU cc_start: 0.7771 (pm20) cc_final: 0.7514 (pm20) REVERT: D 50 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7316 (ptt180) REVERT: E 74 PRO cc_start: 0.8298 (Cg_endo) cc_final: 0.8078 (Cg_exo) REVERT: F 295 TYR cc_start: 0.8560 (m-80) cc_final: 0.8330 (m-80) REVERT: G 241 GLN cc_start: 0.7527 (pm20) cc_final: 0.7212 (mt0) REVERT: H 259 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7359 (ptmt) REVERT: H 271 TYR cc_start: 0.8705 (p90) cc_final: 0.8317 (p90) outliers start: 24 outliers final: 21 residues processed: 155 average time/residue: 0.4350 time to fit residues: 102.4624 Evaluate side-chains 155 residues out of total 2395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 72 optimal weight: 0.0070 chunk 217 optimal weight: 6.9990 chunk 34 optimal weight: 40.0000 chunk 65 optimal weight: 0.0570 chunk 236 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.0170 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098260 restraints weight = 35094.803| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.81 r_work: 0.3060 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.7817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22729 Z= 0.124 Angle : 0.483 11.497 30922 Z= 0.253 Chirality : 0.038 0.203 3215 Planarity : 0.003 0.070 4018 Dihedral : 13.534 156.270 4141 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.31 % Allowed : 15.98 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2939 helix: 2.25 (0.18), residues: 927 sheet: 0.72 (0.25), residues: 448 loop : -1.96 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 147 HIS 0.004 0.001 HIS B 196 PHE 0.007 0.001 PHE H 147 TYR 0.022 0.001 TYR C 305 ARG 0.012 0.000 ARG C 184 =============================================================================== Job complete usr+sys time: 4610.88 seconds wall clock time: 84 minutes 19.46 seconds (5059.46 seconds total)