Starting phenix.real_space_refine on Sun Feb 18 18:56:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b44_7048/02_2024/6b44_7048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b44_7048/02_2024/6b44_7048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b44_7048/02_2024/6b44_7048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b44_7048/02_2024/6b44_7048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b44_7048/02_2024/6b44_7048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b44_7048/02_2024/6b44_7048.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.757 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 114 5.49 5 S 18 5.16 5 C 13604 2.51 5 N 4284 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 207": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" 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: 22681 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2079 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 310} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1373 Unresolved non-hydrogen angles: 1987 Unresolved non-hydrogen dihedrals: 884 Unresolved non-hydrogen chiralities: 392 Planarities with less than four sites: {'GLN:plan1': 29, 'ASP:plan': 20, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 9, 'HIS:plan': 9, 'PHE:plan': 11, 'GLU:plan': 24, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 726 Chain: "B" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2374 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2561 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2566 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2557 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2569 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 761 Classifications: {'peptide': 189} Incomplete info: {'backbone_only': 173} Link IDs: {'PTRANS': 15, 'TRANS': 173} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 803 Unresolved non-hydrogen angles: 1149 Unresolved non-hydrogen dihedrals: 531 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: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1276 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 13, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 20, 'rna3p': 39} Chain: "N" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 850 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "O" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 262 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 12.80, per 1000 atoms: 0.56 Number of scatterers: 22681 At special positions: 0 Unit cell: (133.715, 133.715, 182.413, 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 18 16.00 P 114 15.00 O 4661 8.00 N 4284 7.00 C 13604 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: 9.52 Conformation dependent library (CDL) restraints added in 4.4 seconds 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4386 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 38 sheets defined 29.1% alpha, 16.4% beta 30 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 7.85 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 removed outlier: 3.548A pdb=" N GLU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.892A pdb=" N HIS A 74 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.910A pdb=" N LEU A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.775A pdb=" N PHE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 129 through 134 removed outlier: 4.498A pdb=" N ASN A 132 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 195 through 208 removed outlier: 3.711A pdb=" N GLU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 4.377A pdb=" N ARG A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 4.265A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 317 through 320 removed outlier: 3.646A pdb=" N GLN A 320 " --> pdb=" O ALA A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.961A pdb=" N VAL A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 386 through 399 removed outlier: 4.023A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 398 " --> pdb=" O TRP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 411 through 429 removed outlier: 5.072A pdb=" N GLU A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 46 removed outlier: 3.973A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.917A pdb=" N ILE B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 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 190 through 196 removed outlier: 3.756A pdb=" N GLN B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.710A pdb=" N LEU B 214 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.616A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'C' and resid 111 through 128 removed outlier: 3.592A pdb=" N ARG C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLN C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.853A pdb=" N ARG C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 204 removed outlier: 3.849A pdb=" N LEU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 264 removed outlier: 4.404A pdb=" N ILE C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 313 removed outlier: 4.352A pdb=" N ASP C 309 " --> pdb=" O TYR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'D' and resid 111 through 127 removed outlier: 3.705A pdb=" N GLN D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 removed outlier: 3.507A pdb=" N LEU D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.839A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 removed outlier: 4.601A pdb=" N ASP D 309 " --> pdb=" O TYR D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.657A pdb=" N GLN E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.906A pdb=" N GLN E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN E 129 " --> pdb=" O TYR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.586A pdb=" N ARG E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.633A pdb=" N LEU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.993A pdb=" N LEU E 277 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 removed outlier: 4.231A pdb=" N SER E 287 " --> pdb=" O PRO E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 removed outlier: 4.084A pdb=" N ASP E 309 " --> pdb=" O TYR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.566A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 Processing helix chain 'F' and resid 65 through 73 Processing helix chain 'F' and resid 111 through 129 removed outlier: 3.606A pdb=" N ASN F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP F 128 " --> pdb=" O THR F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.670A pdb=" N ARG F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 204 removed outlier: 3.954A pdb=" N LEU F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 303 through 313 removed outlier: 4.002A pdb=" N ASP F 309 " --> pdb=" O TYR F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.860A pdb=" N HIS F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 39 removed outlier: 4.422A pdb=" N GLU G 38 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP G 39 " --> pdb=" O SER G 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 35 through 39' Processing helix chain 'G' and resid 66 through 71 removed outlier: 3.839A pdb=" N ILE G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 127 Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.622A pdb=" N ARG G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 204 removed outlier: 3.747A pdb=" N ASP G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G 194 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU G 198 " --> pdb=" O ALA G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 265 removed outlier: 3.558A pdb=" N ILE G 260 " --> pdb=" O HIS G 256 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 removed outlier: 4.530A pdb=" N ASP G 309 " --> pdb=" O TYR G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 removed outlier: 3.836A pdb=" N TYR G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 39 removed outlier: 4.274A pdb=" N GLU H 38 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TRP H 39 " --> pdb=" O SER H 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 35 through 39' Processing helix chain 'H' and resid 58 through 62 removed outlier: 4.032A pdb=" N ASP H 61 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG H 62 " --> pdb=" O THR H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 58 through 62' Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.644A pdb=" N GLN H 120 " --> pdb=" O ASP H 116 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP H 128 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN H 129 " --> pdb=" O TYR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 4.065A pdb=" N ARG H 137 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN H 141 " --> pdb=" O ARG H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 204 removed outlier: 4.202A pdb=" N ALA H 194 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU H 198 " --> pdb=" O ALA H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 removed outlier: 3.513A pdb=" N TYR H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU H 330 " --> pdb=" O VAL H 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 30 removed outlier: 4.813A pdb=" N VAL L 23 " --> pdb=" O GLN L 19 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 77 removed outlier: 4.055A pdb=" N LEU L 76 " --> pdb=" O ARG L 73 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU L 77 " --> pdb=" O PRO L 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 73 through 77' Processing helix chain 'L' and resid 78 through 82 removed outlier: 4.240A pdb=" N ASP L 81 " --> pdb=" O GLY L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 120 removed outlier: 4.429A pdb=" N ARG L 118 " --> pdb=" O ARG L 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.744A pdb=" N ASP A 107 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 8.376A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.633A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE B 219 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A 234 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS B 217 " --> pdb=" O GLU A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.576A pdb=" N GLN A 241 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 262 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.519A pdb=" N ARG B 65 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 106 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 159 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'B' and resid 185 through 188 removed outlier: 3.571A pdb=" N VAL B 187 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 288 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 304 through 305 Processing sheet with id=AA9, first strand: chain 'C' and resid 23 through 25 removed outlier: 4.198A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.205A pdb=" N VAL C 79 " --> pdb=" O LYS C 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.676A pdb=" N VAL C 214 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 161 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 216 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU C 159 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG C 172 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.676A pdb=" N VAL C 214 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 161 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 216 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU C 159 " --> pdb=" O PHE C 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.223A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.484A pdb=" N HIS D 164 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 25 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ALA D 253 " --> pdb=" O MET D 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 249 " --> pdb=" O ALA D 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 287 through 288 removed outlier: 4.260A pdb=" N VAL D 288 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.523A pdb=" N VAL E 99 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL E 158 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP E 177 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE E 162 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.533A pdb=" N ILE E 255 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 44 through 52 removed outlier: 4.619A pdb=" N ALA E 82 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.837A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 334 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.449A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA F 157 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG F 172 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 20 removed outlier: 5.066A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 252 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 44 through 51 Processing sheet with id=AC5, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC6, first strand: chain 'F' and resid 287 through 288 removed outlier: 3.525A pdb=" N LYS F 293 " --> pdb=" O VAL F 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 13 through 14 Processing sheet with id=AC8, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.424A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL G 160 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG G 175 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE G 162 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA G 173 " --> pdb=" O ILE G 162 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS G 164 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.791A pdb=" N ALA G 253 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 45 through 52 removed outlier: 3.790A pdb=" N ASN G 75 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA G 82 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD3, first strand: chain 'G' and resid 287 through 288 Processing sheet with id=AD4, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.538A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.933A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL H 158 " --> pdb=" O ASP H 177 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP H 177 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL H 160 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG H 175 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE H 162 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA H 173 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS H 164 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.527A pdb=" N ILE H 255 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA H 253 " --> pdb=" O MET H 25 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 45 through 52 removed outlier: 4.429A pdb=" N ALA H 82 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AD9, first strand: chain 'H' and resid 287 through 288 removed outlier: 3.528A pdb=" N LYS H 293 " --> pdb=" O VAL H 288 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.190A pdb=" N TYR L 4 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 41 through 42 removed outlier: 3.543A pdb=" N HIS L 61 " --> pdb=" O GLY L 41 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 1989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 7.78 Time building geometry restraints manager: 10.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6685 1.33 - 1.46: 5321 1.46 - 1.58: 11067 1.58 - 1.70: 225 1.70 - 1.82: 27 Bond restraints: 23325 Sorted by residual: bond pdb=" C PHE B 152 " pdb=" N PRO B 153 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.41e+00 bond pdb=" CB THR G 289 " pdb=" CG2 THR G 289 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CG1 ILE E 260 " pdb=" CD1 ILE E 260 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.34e+00 bond pdb=" C TRP C 39 " pdb=" N PRO C 40 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.87e+00 bond pdb=" CB ILE C 327 " pdb=" CG2 ILE C 327 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 ... (remaining 23320 not shown) Histogram of bond angle deviations from ideal: 97.17 - 105.22: 810 105.22 - 113.28: 12162 113.28 - 121.33: 12108 121.33 - 129.38: 6655 129.38 - 137.44: 222 Bond angle restraints: 31957 Sorted by residual: angle pdb=" C ARG D 250 " pdb=" N ASP D 251 " pdb=" CA ASP D 251 " ideal model delta sigma weight residual 121.54 132.02 -10.48 1.91e+00 2.74e-01 3.01e+01 angle pdb=" N ILE E 267 " pdb=" CA ILE E 267 " pdb=" C ILE E 267 " ideal model delta sigma weight residual 112.96 107.51 5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" C ARG F 250 " pdb=" N ASP F 251 " pdb=" CA ASP F 251 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 109.34 98.77 10.57 2.08e+00 2.31e-01 2.58e+01 angle pdb=" C ARG G 250 " pdb=" N ASP G 251 " pdb=" CA ASP G 251 " ideal model delta sigma weight residual 122.46 129.62 -7.16 1.41e+00 5.03e-01 2.58e+01 ... (remaining 31952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 12709 35.22 - 70.43: 466 70.43 - 105.65: 38 105.65 - 140.86: 1 140.86 - 176.08: 3 Dihedral angle restraints: 13217 sinusoidal: 5903 harmonic: 7314 Sorted by residual: dihedral pdb=" O4' C M 1 " pdb=" C1' C M 1 " pdb=" N1 C M 1 " pdb=" C2 C M 1 " ideal model delta sinusoidal sigma weight residual 200.00 48.43 151.57 1 1.50e+01 4.44e-03 8.02e+01 dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 51.46 148.54 1 1.50e+01 4.44e-03 7.91e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual 232.00 55.92 176.08 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 13214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2347 0.056 - 0.112: 785 0.112 - 0.168: 170 0.168 - 0.224: 20 0.224 - 0.280: 9 Chirality restraints: 3331 Sorted by residual: chirality pdb=" CB VAL B 322 " pdb=" CA VAL B 322 " pdb=" CG1 VAL B 322 " pdb=" CG2 VAL B 322 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1' C M 16 " pdb=" O4' C M 16 " pdb=" C2' C M 16 " pdb=" N1 C M 16 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ASN A 237 " pdb=" N ASN A 237 " pdb=" C ASN A 237 " pdb=" CB ASN A 237 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 3328 not shown) Planarity restraints: 3954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 311 " 0.031 2.00e-02 2.50e+03 2.48e-02 1.53e+01 pdb=" CG TRP D 311 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP D 311 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 311 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 311 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 311 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 311 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 311 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 311 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 311 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 311 " 0.027 2.00e-02 2.50e+03 2.24e-02 1.25e+01 pdb=" CG TRP E 311 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP E 311 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 311 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 311 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 311 " 0.002 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 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 311 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 311 " 0.030 2.00e-02 2.50e+03 2.16e-02 1.17e+01 pdb=" CG TRP F 311 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP F 311 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP F 311 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 311 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 311 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP F 311 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 311 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 311 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 311 " 0.005 2.00e-02 2.50e+03 ... (remaining 3951 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4130 2.77 - 3.30: 19156 3.30 - 3.83: 37114 3.83 - 4.37: 43862 4.37 - 4.90: 72597 Nonbonded interactions: 176859 Sorted by model distance: nonbonded pdb=" OD1 ASN B 269 " pdb=" OG SER H 10 " model vdw 2.237 2.440 nonbonded pdb=" O GLY L 152 " pdb=" O2' G M 40 " model vdw 2.284 2.440 nonbonded pdb=" O ALA B 270 " pdb=" ND2 ASN H 110 " model vdw 2.285 2.520 nonbonded pdb=" O GLU H 283 " pdb=" OH TYR H 325 " model vdw 2.291 2.440 nonbonded pdb=" OE1 GLN D 229 " pdb=" O2' U M 33 " model vdw 2.291 2.440 ... (remaining 176854 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.470 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 67.150 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.090 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:15.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 23325 Z= 0.421 Angle : 0.993 17.136 31957 Z= 0.543 Chirality : 0.058 0.280 3331 Planarity : 0.007 0.071 3954 Dihedral : 16.386 176.078 8831 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 0.43 % Allowed : 3.24 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.46 (0.12), residues: 2855 helix: -3.30 (0.12), residues: 772 sheet: -1.45 (0.25), residues: 401 loop : -3.33 (0.12), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.005 TRP D 311 HIS 0.013 0.003 HIS A 188 PHE 0.039 0.004 PHE H 336 TYR 0.031 0.003 TYR G 138 ARG 0.021 0.001 ARG E 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 264 time to evaluate : 2.980 Fit side-chains REVERT: A 242 LYS cc_start: 0.8078 (mptp) cc_final: 0.7866 (mmmt) REVERT: B 159 LEU cc_start: 0.5757 (pt) cc_final: 0.5407 (mt) REVERT: B 263 LEU cc_start: 0.7051 (mm) cc_final: 0.6710 (tp) REVERT: C 172 ARG cc_start: 0.4562 (tpt170) cc_final: 0.2757 (mtt90) REVERT: C 271 TYR cc_start: 0.3148 (p90) cc_final: 0.1680 (p90) REVERT: D 30 TRP cc_start: 0.6210 (m100) cc_final: 0.5979 (m100) REVERT: D 293 LYS cc_start: 0.7366 (tmmm) cc_final: 0.7099 (tppp) REVERT: H 175 ARG cc_start: 0.7026 (mtp85) cc_final: 0.6822 (ttm-80) REVERT: L -1 MET cc_start: 0.1241 (mmm) cc_final: -0.0394 (mmm) outliers start: 8 outliers final: 2 residues processed: 272 average time/residue: 1.6739 time to fit residues: 507.8825 Evaluate side-chains 134 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 0.9990 chunk 223 optimal weight: 7.9990 chunk 124 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 231 optimal weight: 0.9990 chunk 89 optimal weight: 40.0000 chunk 140 optimal weight: 0.4980 chunk 172 optimal weight: 5.9990 chunk 267 optimal weight: 50.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 82 ASN B 104 HIS B 114 HIS B 124 GLN B 149 ASN B 172 ASN B 194 GLN B 305 HIS C 144 ASN D 83 ASN D 223 GLN D 324 HIS D 329 ASN E 127 ASN E 164 HIS E 167 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN E 324 HIS F 110 ASN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 GLN G 83 ASN G 110 ASN G 120 GLN G 129 GLN G 164 HIS H 223 GLN H 310 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23325 Z= 0.182 Angle : 0.607 12.700 31957 Z= 0.326 Chirality : 0.042 0.208 3331 Planarity : 0.005 0.054 3954 Dihedral : 18.994 179.871 4653 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.27 % Allowed : 9.24 % Favored : 88.49 % 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: -3.25 (0.14), residues: 2855 helix: -1.76 (0.16), residues: 774 sheet: -0.79 (0.25), residues: 392 loop : -2.83 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 311 HIS 0.008 0.001 HIS A 188 PHE 0.018 0.002 PHE H 336 TYR 0.015 0.002 TYR F 285 ARG 0.011 0.001 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 160 time to evaluate : 2.724 Fit side-chains REVERT: A 234 GLU cc_start: 0.6397 (tp30) cc_final: 0.6031 (tp30) REVERT: A 242 LYS cc_start: 0.7966 (mptp) cc_final: 0.7633 (mmmt) REVERT: B 118 LEU cc_start: 0.5893 (tp) cc_final: 0.5471 (mt) REVERT: B 159 LEU cc_start: 0.5876 (pt) cc_final: 0.5301 (mt) REVERT: C 172 ARG cc_start: 0.3812 (tpt170) cc_final: 0.2355 (mtt90) REVERT: C 203 LEU cc_start: 0.4945 (OUTLIER) cc_final: 0.4630 (pt) REVERT: D 191 GLU cc_start: 0.6828 (pt0) cc_final: 0.6596 (mp0) REVERT: F 38 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6782 (pp20) REVERT: G 221 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6846 (m-30) REVERT: H 175 ARG cc_start: 0.7005 (mtp85) cc_final: 0.6792 (ttm-80) REVERT: L -1 MET cc_start: 0.1243 (mmm) cc_final: -0.0375 (mmm) outliers start: 42 outliers final: 17 residues processed: 191 average time/residue: 1.4911 time to fit residues: 324.0312 Evaluate side-chains 137 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 221 ASP Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 268 optimal weight: 50.0000 chunk 289 optimal weight: 50.0000 chunk 239 optimal weight: 6.9990 chunk 266 optimal weight: 50.0000 chunk 91 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN B 104 HIS B 293 HIS B 305 HIS C 151 ASN D 72 GLN D 140 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN F 129 GLN F 324 HIS G 120 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23325 Z= 0.329 Angle : 0.682 16.370 31957 Z= 0.362 Chirality : 0.046 0.235 3331 Planarity : 0.005 0.051 3954 Dihedral : 19.001 179.181 4650 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 3.84 % Allowed : 10.32 % Favored : 85.85 % 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: -2.89 (0.14), residues: 2855 helix: -1.18 (0.17), residues: 781 sheet: -0.68 (0.27), residues: 363 loop : -2.71 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 311 HIS 0.009 0.002 HIS A 188 PHE 0.019 0.002 PHE H 336 TYR 0.024 0.002 TYR F 305 ARG 0.008 0.001 ARG G 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 125 time to evaluate : 2.443 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.3984 (mmtt) cc_final: 0.3401 (mmmt) REVERT: A 242 LYS cc_start: 0.7956 (mptp) cc_final: 0.7600 (mmmt) REVERT: B 97 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.7989 (mp) REVERT: B 118 LEU cc_start: 0.5975 (tp) cc_final: 0.5564 (mt) REVERT: C 121 THR cc_start: 0.1750 (OUTLIER) cc_final: 0.1422 (p) REVERT: C 159 GLU cc_start: 0.4878 (mt-10) cc_final: 0.3101 (pp20) REVERT: C 172 ARG cc_start: 0.3707 (tpt170) cc_final: 0.2205 (mtt90) REVERT: C 203 LEU cc_start: 0.4960 (OUTLIER) cc_final: 0.4675 (pt) REVERT: D 241 GLN cc_start: 0.5755 (OUTLIER) cc_final: 0.5142 (mm-40) REVERT: D 251 ASP cc_start: 0.5896 (p0) cc_final: 0.4721 (p0) REVERT: D 267 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7468 (mm) REVERT: E 221 ASP cc_start: 0.7451 (m-30) cc_final: 0.7244 (m-30) REVERT: F 38 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6872 (pp20) REVERT: F 66 LYS cc_start: 0.5299 (OUTLIER) cc_final: 0.4989 (mmtt) REVERT: G 283 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6630 (mt-10) REVERT: H 175 ARG cc_start: 0.7119 (mtp85) cc_final: 0.6854 (ttm-80) REVERT: L -1 MET cc_start: 0.1667 (mmm) cc_final: -0.0209 (mmm) outliers start: 71 outliers final: 25 residues processed: 182 average time/residue: 1.4138 time to fit residues: 293.4620 Evaluate side-chains 145 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 139 optimal weight: 0.4980 chunk 29 optimal weight: 50.0000 chunk 128 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 269 optimal weight: 50.0000 chunk 285 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS B 293 HIS B 305 HIS D 72 GLN D 140 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23325 Z= 0.261 Angle : 0.623 14.148 31957 Z= 0.332 Chirality : 0.043 0.215 3331 Planarity : 0.005 0.048 3954 Dihedral : 18.903 179.796 4650 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.84 % Allowed : 11.45 % Favored : 84.71 % 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: -2.57 (0.15), residues: 2855 helix: -0.79 (0.18), residues: 778 sheet: -0.63 (0.26), residues: 382 loop : -2.55 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 311 HIS 0.009 0.001 HIS B 305 PHE 0.014 0.002 PHE H 336 TYR 0.024 0.002 TYR C 271 ARG 0.006 0.001 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 124 time to evaluate : 2.644 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.4030 (mmtp) cc_final: 0.3390 (mmmt) REVERT: A 242 LYS cc_start: 0.7897 (mptp) cc_final: 0.7350 (mmmt) REVERT: B 97 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 118 LEU cc_start: 0.6006 (tp) cc_final: 0.5573 (mt) REVERT: C 121 THR cc_start: 0.1712 (OUTLIER) cc_final: 0.1390 (p) REVERT: C 133 GLU cc_start: 0.4830 (OUTLIER) cc_final: 0.4101 (mm-30) REVERT: C 203 LEU cc_start: 0.4966 (OUTLIER) cc_final: 0.4673 (pt) REVERT: C 231 LEU cc_start: 0.2103 (OUTLIER) cc_final: -0.0109 (pt) REVERT: C 274 GLU cc_start: 0.5374 (OUTLIER) cc_final: 0.5143 (mt-10) REVERT: C 295 TYR cc_start: 0.5840 (m-80) cc_final: 0.4848 (m-80) REVERT: D 250 ARG cc_start: 0.6886 (ppt90) cc_final: 0.6397 (mtm110) REVERT: D 267 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7508 (mm) REVERT: F 38 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6871 (pp20) REVERT: F 197 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: G 283 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6657 (mt-10) REVERT: H 175 ARG cc_start: 0.7106 (mtp85) cc_final: 0.6869 (ttm-80) REVERT: L -1 MET cc_start: 0.1653 (mmm) cc_final: -0.0196 (mmm) outliers start: 71 outliers final: 32 residues processed: 184 average time/residue: 1.3086 time to fit residues: 277.7245 Evaluate side-chains 156 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 4 optimal weight: 50.0000 chunk 212 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 145 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 293 HIS B 305 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23325 Z= 0.214 Angle : 0.579 12.379 31957 Z= 0.309 Chirality : 0.042 0.211 3331 Planarity : 0.004 0.046 3954 Dihedral : 18.818 179.392 4650 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.89 % Allowed : 12.37 % Favored : 83.74 % 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: -2.31 (0.15), residues: 2855 helix: -0.45 (0.19), residues: 777 sheet: -0.52 (0.27), residues: 377 loop : -2.43 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 311 HIS 0.008 0.001 HIS B 305 PHE 0.012 0.001 PHE C 95 TYR 0.018 0.002 TYR C 271 ARG 0.009 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 129 time to evaluate : 2.509 Fit side-chains REVERT: A 216 LYS cc_start: 0.3972 (mmtp) cc_final: 0.3370 (mmmt) REVERT: A 242 LYS cc_start: 0.7756 (mptp) cc_final: 0.7475 (mmmt) REVERT: B 97 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7859 (mp) REVERT: B 118 LEU cc_start: 0.5843 (tp) cc_final: 0.5568 (mt) REVERT: C 121 THR cc_start: 0.1572 (OUTLIER) cc_final: 0.1231 (p) REVERT: C 172 ARG cc_start: 0.3383 (tpt170) cc_final: 0.2356 (tpm-80) REVERT: C 203 LEU cc_start: 0.5040 (OUTLIER) cc_final: 0.4750 (pt) REVERT: C 231 LEU cc_start: 0.2106 (OUTLIER) cc_final: -0.0053 (pt) REVERT: C 271 TYR cc_start: 0.3543 (OUTLIER) cc_final: 0.1820 (p90) REVERT: C 295 TYR cc_start: 0.5740 (m-80) cc_final: 0.5424 (m-80) REVERT: D 251 ASP cc_start: 0.5632 (p0) cc_final: 0.5390 (p0) REVERT: D 267 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7555 (mm) REVERT: D 283 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6138 (mm-30) REVERT: D 302 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6287 (mm) REVERT: F 38 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6848 (pp20) REVERT: F 197 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: H 175 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6862 (ttm-80) REVERT: L -1 MET cc_start: 0.1606 (mmm) cc_final: -0.0240 (mmm) outliers start: 72 outliers final: 35 residues processed: 188 average time/residue: 1.3656 time to fit residues: 293.3820 Evaluate side-chains 162 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 117 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 TRP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 87 ASP Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 40.0000 chunk 256 optimal weight: 0.0370 chunk 56 optimal weight: 30.0000 chunk 167 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 305 HIS ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN G 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23325 Z= 0.196 Angle : 0.568 14.101 31957 Z= 0.301 Chirality : 0.041 0.205 3331 Planarity : 0.004 0.048 3954 Dihedral : 18.731 179.287 4650 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.46 % Allowed : 13.67 % 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: -2.11 (0.15), residues: 2855 helix: -0.18 (0.19), residues: 776 sheet: -0.49 (0.26), residues: 397 loop : -2.35 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 311 HIS 0.007 0.001 HIS B 305 PHE 0.012 0.001 PHE C 95 TYR 0.017 0.001 TYR C 271 ARG 0.016 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 131 time to evaluate : 2.476 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.4047 (mmtp) cc_final: 0.3416 (mmmt) REVERT: A 242 LYS cc_start: 0.7702 (mptp) cc_final: 0.7402 (mmmt) REVERT: B 97 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7846 (mp) REVERT: B 118 LEU cc_start: 0.5855 (tp) cc_final: 0.5588 (mt) REVERT: C 172 ARG cc_start: 0.3335 (tpt170) cc_final: 0.2305 (tpm-80) REVERT: C 203 LEU cc_start: 0.5086 (OUTLIER) cc_final: 0.4784 (pt) REVERT: C 231 LEU cc_start: 0.2170 (OUTLIER) cc_final: -0.0087 (pt) REVERT: C 271 TYR cc_start: 0.3363 (OUTLIER) cc_final: 0.1488 (p90) REVERT: D 25 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.4441 (mmt) REVERT: D 267 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7522 (mm) REVERT: D 283 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6241 (mm-30) REVERT: D 302 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6132 (mm) REVERT: F 38 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6825 (pp20) REVERT: F 197 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: H 175 ARG cc_start: 0.7088 (mtp85) cc_final: 0.6853 (ttm-80) REVERT: L -1 MET cc_start: 0.1407 (mmm) cc_final: -0.0492 (mmm) outliers start: 64 outliers final: 36 residues processed: 183 average time/residue: 1.3061 time to fit residues: 276.1515 Evaluate side-chains 166 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 120 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 TRP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 50.0000 chunk 32 optimal weight: 50.0000 chunk 162 optimal weight: 0.6980 chunk 208 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 284 optimal weight: 20.0000 chunk 177 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN B 293 HIS B 305 HIS ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 GLN G 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23325 Z= 0.232 Angle : 0.590 14.129 31957 Z= 0.312 Chirality : 0.042 0.210 3331 Planarity : 0.004 0.048 3954 Dihedral : 18.736 179.700 4650 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.67 % Allowed : 13.83 % Favored : 82.50 % 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: -2.08 (0.15), residues: 2855 helix: -0.15 (0.19), residues: 777 sheet: -0.44 (0.27), residues: 382 loop : -2.33 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 311 HIS 0.007 0.001 HIS B 305 PHE 0.013 0.002 PHE D 216 TYR 0.018 0.002 TYR C 271 ARG 0.012 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 121 time to evaluate : 2.515 Fit side-chains REVERT: A 216 LYS cc_start: 0.4090 (mmtp) cc_final: 0.3469 (mmmt) REVERT: A 242 LYS cc_start: 0.7689 (mptp) cc_final: 0.7403 (mmmt) REVERT: B 97 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7840 (mp) REVERT: B 118 LEU cc_start: 0.5763 (tp) cc_final: 0.5563 (mt) REVERT: C 121 THR cc_start: 0.1485 (OUTLIER) cc_final: 0.1192 (p) REVERT: C 172 ARG cc_start: 0.3461 (tpt170) cc_final: 0.2441 (tpm-80) REVERT: C 203 LEU cc_start: 0.5115 (OUTLIER) cc_final: 0.4812 (pt) REVERT: C 231 LEU cc_start: 0.2201 (OUTLIER) cc_final: -0.0125 (pt) REVERT: D 25 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.4467 (mmt) REVERT: D 283 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6260 (mm-30) REVERT: D 302 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6118 (mm) REVERT: F 38 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6836 (pp20) REVERT: F 197 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: H 175 ARG cc_start: 0.7104 (mtp85) cc_final: 0.6862 (ttm-80) REVERT: L -1 MET cc_start: 0.1518 (mmm) cc_final: -0.0327 (mmm) outliers start: 68 outliers final: 37 residues processed: 177 average time/residue: 1.2393 time to fit residues: 254.4281 Evaluate side-chains 163 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 117 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 223 optimal weight: 0.0570 chunk 258 optimal weight: 5.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 305 HIS C 324 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN G 129 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23325 Z= 0.153 Angle : 0.536 13.327 31957 Z= 0.284 Chirality : 0.040 0.191 3331 Planarity : 0.004 0.049 3954 Dihedral : 18.605 178.852 4650 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.03 % Allowed : 14.96 % Favored : 82.01 % 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: -1.86 (0.16), residues: 2855 helix: 0.10 (0.19), residues: 782 sheet: -0.33 (0.27), residues: 388 loop : -2.23 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 311 HIS 0.006 0.001 HIS B 305 PHE 0.019 0.001 PHE C 304 TYR 0.014 0.001 TYR C 271 ARG 0.009 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 128 time to evaluate : 2.390 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.3838 (mmtp) cc_final: 0.3319 (mmmt) REVERT: A 242 LYS cc_start: 0.7604 (mptp) cc_final: 0.7163 (mmmt) REVERT: B 97 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7769 (mp) REVERT: C 77 GLN cc_start: 0.1597 (mm-40) cc_final: 0.0475 (pm20) REVERT: C 121 THR cc_start: 0.1375 (OUTLIER) cc_final: 0.1042 (p) REVERT: C 203 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.4857 (pt) REVERT: C 218 ARG cc_start: 0.1938 (mtt90) cc_final: 0.0420 (pmm150) REVERT: C 231 LEU cc_start: 0.2307 (OUTLIER) cc_final: -0.0144 (pt) REVERT: D 283 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6211 (mm-30) REVERT: D 302 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5958 (mm) REVERT: F 38 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6750 (pp20) REVERT: H 175 ARG cc_start: 0.7060 (mtp85) cc_final: 0.6857 (ttm-80) REVERT: H 241 GLN cc_start: 0.7989 (pt0) cc_final: 0.7758 (pm20) REVERT: L -1 MET cc_start: 0.1412 (mmm) cc_final: -0.0440 (mmm) outliers start: 56 outliers final: 28 residues processed: 175 average time/residue: 1.3073 time to fit residues: 263.1489 Evaluate side-chains 157 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 TRP Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 50.0000 chunk 248 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 159 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 280 optimal weight: 0.3980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 305 HIS D 37 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 GLN G 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23325 Z= 0.208 Angle : 0.570 13.682 31957 Z= 0.301 Chirality : 0.042 0.196 3331 Planarity : 0.004 0.047 3954 Dihedral : 18.616 179.430 4650 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.19 % Allowed : 14.91 % Favored : 81.90 % 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: -1.87 (0.15), residues: 2855 helix: 0.10 (0.19), residues: 788 sheet: -0.30 (0.27), residues: 380 loop : -2.25 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 311 HIS 0.008 0.001 HIS B 305 PHE 0.029 0.002 PHE C 304 TYR 0.015 0.001 TYR C 271 ARG 0.020 0.000 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 123 time to evaluate : 2.505 Fit side-chains REVERT: A 216 LYS cc_start: 0.3999 (mmtp) cc_final: 0.3411 (mmmt) REVERT: A 242 LYS cc_start: 0.7567 (mptp) cc_final: 0.7314 (mmmt) REVERT: B 97 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7715 (mp) REVERT: B 189 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6934 (tmt-80) REVERT: C 121 THR cc_start: 0.1578 (OUTLIER) cc_final: 0.1268 (p) REVERT: C 203 LEU cc_start: 0.5072 (OUTLIER) cc_final: 0.4777 (pt) REVERT: C 231 LEU cc_start: 0.2381 (OUTLIER) cc_final: -0.0094 (pt) REVERT: D 116 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7501 (m-30) REVERT: D 283 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6287 (mm-30) REVERT: D 302 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6018 (mm) REVERT: F 38 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6781 (pp20) REVERT: F 300 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6734 (pt0) REVERT: H 175 ARG cc_start: 0.7078 (mtp85) cc_final: 0.6869 (ttm-80) REVERT: H 241 GLN cc_start: 0.7994 (pt0) cc_final: 0.7743 (pm20) REVERT: L -1 MET cc_start: 0.1575 (mmm) cc_final: -0.0293 (mmm) outliers start: 59 outliers final: 32 residues processed: 173 average time/residue: 1.2931 time to fit residues: 257.9643 Evaluate side-chains 162 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 120 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 300 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 chunk 270 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 305 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 GLN G 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23325 Z= 0.157 Angle : 0.540 13.163 31957 Z= 0.285 Chirality : 0.040 0.187 3331 Planarity : 0.004 0.052 3954 Dihedral : 18.552 178.971 4650 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.38 % Allowed : 15.99 % Favored : 81.63 % 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: -1.72 (0.16), residues: 2855 helix: 0.25 (0.19), residues: 787 sheet: -0.23 (0.28), residues: 374 loop : -2.17 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 30 HIS 0.006 0.001 HIS B 305 PHE 0.019 0.001 PHE C 304 TYR 0.015 0.001 TYR C 271 ARG 0.017 0.000 ARG D 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 2.539 Fit side-chains revert: symmetry clash REVERT: A 216 LYS cc_start: 0.3927 (mmtp) cc_final: 0.3356 (mmmt) REVERT: A 237 ASN cc_start: 0.7165 (OUTLIER) cc_final: 0.6266 (t0) REVERT: A 242 LYS cc_start: 0.7579 (mptp) cc_final: 0.7224 (mmmt) REVERT: B 189 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6987 (tmt-80) REVERT: C 121 THR cc_start: 0.1394 (OUTLIER) cc_final: 0.1042 (p) REVERT: C 203 LEU cc_start: 0.5113 (OUTLIER) cc_final: 0.4843 (pt) REVERT: C 231 LEU cc_start: 0.2415 (OUTLIER) cc_final: -0.0116 (pt) REVERT: D 25 MET cc_start: 0.5854 (OUTLIER) cc_final: 0.4453 (mmt) REVERT: D 283 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6292 (mm-30) REVERT: D 302 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.5972 (mm) REVERT: F 38 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6751 (pp20) REVERT: F 300 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6740 (pt0) REVERT: H 241 GLN cc_start: 0.7967 (pt0) cc_final: 0.7732 (pm20) REVERT: L -1 MET cc_start: 0.1462 (mmm) cc_final: -0.0414 (mmm) outliers start: 44 outliers final: 28 residues processed: 164 average time/residue: 1.4995 time to fit residues: 282.1455 Evaluate side-chains 156 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 174 TRP Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 300 GLN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 0.0570 chunk 215 optimal weight: 10.0000 chunk 34 optimal weight: 50.0000 chunk 65 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 29 optimal weight: 70.0000 chunk 43 optimal weight: 0.7980 chunk 205 optimal weight: 9.9990 chunk 13 optimal weight: 50.0000 overall best weight: 4.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 305 HIS D 37 GLN D 140 HIS ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 GLN G 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.170244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.141269 restraints weight = 42996.761| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.19 r_work: 0.3704 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23325 Z= 0.249 Angle : 0.607 13.874 31957 Z= 0.319 Chirality : 0.043 0.202 3331 Planarity : 0.004 0.052 3954 Dihedral : 18.636 179.867 4650 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.08 % Allowed : 15.61 % Favored : 81.31 % 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: -1.88 (0.15), residues: 2855 helix: 0.05 (0.19), residues: 796 sheet: -0.33 (0.26), residues: 395 loop : -2.25 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 311 HIS 0.008 0.001 HIS B 305 PHE 0.022 0.002 PHE C 304 TYR 0.022 0.002 TYR C 271 ARG 0.017 0.001 ARG D 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6320.15 seconds wall clock time: 114 minutes 1.95 seconds (6841.95 seconds total)